Starting phenix.real_space_refine on Fri Oct 11 15:16:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6h_44259/10_2024/9b6h_44259_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6h_44259/10_2024/9b6h_44259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6h_44259/10_2024/9b6h_44259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6h_44259/10_2024/9b6h_44259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6h_44259/10_2024/9b6h_44259_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b6h_44259/10_2024/9b6h_44259_trim.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 120 5.16 5 C 19104 2.51 5 N 4680 2.21 5 O 5064 1.98 5 F 24 1.80 5 H 26696 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 55692 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 13754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 934, 13754 Classifications: {'peptide': 934} Link IDs: {'PTRANS': 23, 'TRANS': 910} Chain breaks: 9 Unresolved non-hydrogen bonds: 556 Unresolved non-hydrogen angles: 685 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 15, 'ASP:plan': 20, 'PHE:plan': 7, 'GLU:plan': 20, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 357 Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 169 Unusual residues: {'NAG': 1, 'T14': 1, 'ULO': 1, 'Y01': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, D Time building chain proxies: 38.70, per 1000 atoms: 0.69 Number of scatterers: 55692 At special positions: 0 Unit cell: (152.28, 152.28, 157.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 120 16.00 P 4 15.00 F 24 9.00 O 5064 8.00 N 4680 7.00 C 19104 6.00 H 26696 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 326 " distance=1.51 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=1.62 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.36 Conformation dependent library (CDL) restraints added in 3.8 seconds 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7120 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 12 sheets defined 72.9% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.84 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 125 through 136 removed outlier: 4.011A pdb=" N HIS A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 Processing helix chain 'A' and resid 187 through 202 Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.852A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.617A pdb=" N SER A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 362 through 369 Processing helix chain 'A' and resid 370 through 387 removed outlier: 4.152A pdb=" N SER A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 419 Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 457 through 469 removed outlier: 4.238A pdb=" N VAL A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 489 through 501 removed outlier: 3.526A pdb=" N PHE A 501 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 516 Processing helix chain 'A' and resid 518 through 534 removed outlier: 4.124A pdb=" N PHE A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 586 through 604 Processing helix chain 'A' and resid 608 through 636 Processing helix chain 'A' and resid 637 through 646 removed outlier: 3.548A pdb=" N GLU A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 663 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 671 through 684 Processing helix chain 'A' and resid 691 through 701 Processing helix chain 'A' and resid 702 through 707 removed outlier: 4.288A pdb=" N GLY A 706 " --> pdb=" O ILE A 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A 707 " --> pdb=" O PRO A 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 702 through 707' Processing helix chain 'A' and resid 723 through 733 Processing helix chain 'A' and resid 733 through 758 Processing helix chain 'A' and resid 765 through 789 Processing helix chain 'A' and resid 790 through 795 Processing helix chain 'A' and resid 796 through 817 Processing helix chain 'A' and resid 823 through 841 Processing helix chain 'A' and resid 841 through 847 removed outlier: 4.207A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 853 through 860 Processing helix chain 'A' and resid 863 through 890 removed outlier: 3.611A pdb=" N VAL A 867 " --> pdb=" O MET A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 904 Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 911 through 913 No H-bonds generated for 'chain 'A' and resid 911 through 913' Processing helix chain 'A' and resid 952 through 969 Proline residue: A 958 - end of helix removed outlier: 3.507A pdb=" N ILE A 969 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 986 Processing helix chain 'A' and resid 987 through 1007 removed outlier: 4.041A pdb=" N ASP A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 993 " --> pdb=" O ASN A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1027 removed outlier: 4.124A pdb=" N VAL A1017 " --> pdb=" O PHE A1013 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE A1018 " --> pdb=" O PRO A1014 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1073 Processing helix chain 'A' and resid 1076 through 1104 removed outlier: 3.673A pdb=" N HIS A1080 " --> pdb=" O GLU A1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 125 through 136 removed outlier: 4.011A pdb=" N HIS B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 216 through 220 Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.852A pdb=" N LEU B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.617A pdb=" N SER B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 343 Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 362 through 369 Processing helix chain 'B' and resid 370 through 387 removed outlier: 4.152A pdb=" N SER B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 418 Processing helix chain 'B' and resid 426 through 436 Processing helix chain 'B' and resid 439 through 446 Processing helix chain 'B' and resid 457 through 469 removed outlier: 4.238A pdb=" N VAL B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 480 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 489 through 501 removed outlier: 3.526A pdb=" N PHE B 501 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 518 through 534 removed outlier: 4.123A pdb=" N PHE B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 586 through 604 Processing helix chain 'B' and resid 608 through 636 Processing helix chain 'B' and resid 637 through 646 removed outlier: 3.548A pdb=" N GLU B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 691 through 701 Processing helix chain 'B' and resid 702 through 707 removed outlier: 4.288A pdb=" N GLY B 706 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS B 707 " --> pdb=" O PRO B 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 702 through 707' Processing helix chain 'B' and resid 723 through 733 Processing helix chain 'B' and resid 733 through 758 Processing helix chain 'B' and resid 765 through 789 Processing helix chain 'B' and resid 790 through 795 Processing helix chain 'B' and resid 796 through 817 Processing helix chain 'B' and resid 823 through 841 Processing helix chain 'B' and resid 841 through 847 removed outlier: 4.206A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 853 through 860 Processing helix chain 'B' and resid 863 through 890 removed outlier: 3.611A pdb=" N VAL B 867 " --> pdb=" O MET B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 904 Processing helix chain 'B' and resid 904 through 910 Processing helix chain 'B' and resid 911 through 913 No H-bonds generated for 'chain 'B' and resid 911 through 913' Processing helix chain 'B' and resid 952 through 969 Proline residue: B 958 - end of helix removed outlier: 3.508A pdb=" N ILE B 969 " --> pdb=" O LEU B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 986 Processing helix chain 'B' and resid 987 through 1007 removed outlier: 4.041A pdb=" N ASP B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 993 " --> pdb=" O ASN B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1027 removed outlier: 4.124A pdb=" N VAL B1017 " --> pdb=" O PHE B1013 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE B1018 " --> pdb=" O PRO B1014 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA B1019 " --> pdb=" O PHE B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1073 Processing helix chain 'B' and resid 1076 through 1104 removed outlier: 3.673A pdb=" N HIS B1080 " --> pdb=" O GLU B1076 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 125 through 136 removed outlier: 4.011A pdb=" N HIS C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 176 Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.851A pdb=" N LEU C 277 " --> pdb=" O VAL C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 removed outlier: 3.617A pdb=" N SER C 322 " --> pdb=" O THR C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 370 through 387 removed outlier: 4.152A pdb=" N SER C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 418 Processing helix chain 'C' and resid 426 through 436 Processing helix chain 'C' and resid 439 through 446 Processing helix chain 'C' and resid 457 through 469 removed outlier: 4.238A pdb=" N VAL C 461 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 483 through 488 Processing helix chain 'C' and resid 489 through 501 removed outlier: 3.526A pdb=" N PHE C 501 " --> pdb=" O PHE C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 518 through 534 removed outlier: 4.123A pdb=" N PHE C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 571 Processing helix chain 'C' and resid 573 through 582 Processing helix chain 'C' and resid 586 through 604 Processing helix chain 'C' and resid 608 through 636 Processing helix chain 'C' and resid 637 through 646 removed outlier: 3.548A pdb=" N GLU C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 663 Processing helix chain 'C' and resid 665 through 670 Processing helix chain 'C' and resid 671 through 684 Processing helix chain 'C' and resid 691 through 701 Processing helix chain 'C' and resid 702 through 707 removed outlier: 4.287A pdb=" N GLY C 706 " --> pdb=" O ILE C 702 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS C 707 " --> pdb=" O PRO C 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 702 through 707' Processing helix chain 'C' and resid 723 through 733 Processing helix chain 'C' and resid 733 through 758 Processing helix chain 'C' and resid 765 through 789 Processing helix chain 'C' and resid 790 through 795 Processing helix chain 'C' and resid 796 through 817 Processing helix chain 'C' and resid 823 through 841 Processing helix chain 'C' and resid 841 through 847 removed outlier: 4.206A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 850 No H-bonds generated for 'chain 'C' and resid 848 through 850' Processing helix chain 'C' and resid 853 through 860 Processing helix chain 'C' and resid 863 through 890 removed outlier: 3.611A pdb=" N VAL C 867 " --> pdb=" O MET C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 904 Processing helix chain 'C' and resid 904 through 910 Processing helix chain 'C' and resid 911 through 913 No H-bonds generated for 'chain 'C' and resid 911 through 913' Processing helix chain 'C' and resid 952 through 969 Proline residue: C 958 - end of helix removed outlier: 3.508A pdb=" N ILE C 969 " --> pdb=" O LEU C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 986 Processing helix chain 'C' and resid 987 through 1007 removed outlier: 4.041A pdb=" N ASP C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 993 " --> pdb=" O ASN C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1027 removed outlier: 4.124A pdb=" N VAL C1017 " --> pdb=" O PHE C1013 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE C1018 " --> pdb=" O PRO C1014 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA C1019 " --> pdb=" O PHE C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1073 Processing helix chain 'C' and resid 1076 through 1104 removed outlier: 3.672A pdb=" N HIS C1080 " --> pdb=" O GLU C1076 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 50 Processing helix chain 'D' and resid 125 through 136 removed outlier: 4.010A pdb=" N HIS D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 176 Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 216 through 220 Processing helix chain 'D' and resid 273 through 288 removed outlier: 3.852A pdb=" N LEU D 277 " --> pdb=" O VAL D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 322 removed outlier: 3.617A pdb=" N SER D 322 " --> pdb=" O THR D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 362 through 369 Processing helix chain 'D' and resid 370 through 387 removed outlier: 4.152A pdb=" N SER D 387 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 418 Processing helix chain 'D' and resid 426 through 436 Processing helix chain 'D' and resid 439 through 446 Processing helix chain 'D' and resid 457 through 469 removed outlier: 4.237A pdb=" N VAL D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 480 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 489 through 501 removed outlier: 3.526A pdb=" N PHE D 501 " --> pdb=" O PHE D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 516 Processing helix chain 'D' and resid 518 through 534 removed outlier: 4.123A pdb=" N PHE D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 571 Processing helix chain 'D' and resid 573 through 582 Processing helix chain 'D' and resid 586 through 604 Processing helix chain 'D' and resid 608 through 636 Processing helix chain 'D' and resid 637 through 646 removed outlier: 3.548A pdb=" N GLU D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 663 Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 671 through 684 Processing helix chain 'D' and resid 691 through 701 Processing helix chain 'D' and resid 702 through 707 removed outlier: 4.288A pdb=" N GLY D 706 " --> pdb=" O ILE D 702 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS D 707 " --> pdb=" O PRO D 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 702 through 707' Processing helix chain 'D' and resid 723 through 733 Processing helix chain 'D' and resid 733 through 758 Processing helix chain 'D' and resid 765 through 789 Processing helix chain 'D' and resid 790 through 795 Processing helix chain 'D' and resid 796 through 817 Processing helix chain 'D' and resid 823 through 841 Processing helix chain 'D' and resid 841 through 847 removed outlier: 4.207A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 850 No H-bonds generated for 'chain 'D' and resid 848 through 850' Processing helix chain 'D' and resid 853 through 860 Processing helix chain 'D' and resid 863 through 890 removed outlier: 3.611A pdb=" N VAL D 867 " --> pdb=" O MET D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 904 Processing helix chain 'D' and resid 904 through 910 Processing helix chain 'D' and resid 911 through 913 No H-bonds generated for 'chain 'D' and resid 911 through 913' Processing helix chain 'D' and resid 952 through 969 Proline residue: D 958 - end of helix removed outlier: 3.507A pdb=" N ILE D 969 " --> pdb=" O LEU D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 986 Processing helix chain 'D' and resid 987 through 1007 removed outlier: 4.042A pdb=" N ASP D 991 " --> pdb=" O GLN D 987 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL D 993 " --> pdb=" O ASN D 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 1012 through 1027 removed outlier: 4.124A pdb=" N VAL D1017 " --> pdb=" O PHE D1013 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N PHE D1018 " --> pdb=" O PRO D1014 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA D1019 " --> pdb=" O PHE D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1073 Processing helix chain 'D' and resid 1076 through 1104 removed outlier: 3.672A pdb=" N HIS D1080 " --> pdb=" O GLU D1076 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 120 Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 180 removed outlier: 3.521A pdb=" N ILE A 146 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 329 removed outlier: 6.349A pdb=" N CYS A 326 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ILE A 394 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL A 328 " --> pdb=" O ILE A 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 120 Processing sheet with id=AA5, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.521A pdb=" N ILE B 146 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 326 through 329 removed outlier: 6.349A pdb=" N CYS B 326 " --> pdb=" O THR B 392 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ILE B 394 " --> pdb=" O CYS B 326 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL B 328 " --> pdb=" O ILE B 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 117 through 120 Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 180 removed outlier: 3.521A pdb=" N ILE C 146 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 326 through 329 removed outlier: 6.348A pdb=" N CYS C 326 " --> pdb=" O THR C 392 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ILE C 394 " --> pdb=" O CYS C 326 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C 328 " --> pdb=" O ILE C 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 117 through 120 Processing sheet with id=AB2, first strand: chain 'D' and resid 178 through 180 removed outlier: 3.520A pdb=" N ILE D 146 " --> pdb=" O VAL D 302 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 326 through 329 removed outlier: 6.349A pdb=" N CYS D 326 " --> pdb=" O THR D 392 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ILE D 394 " --> pdb=" O CYS D 326 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL D 328 " --> pdb=" O ILE D 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 1910 hydrogen bonds defined for protein. 5670 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.83 Time building geometry restraints manager: 14.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 26656 1.03 - 1.24: 2633 1.24 - 1.45: 10270 1.45 - 1.65: 16641 1.65 - 1.86: 192 Bond restraints: 56392 Sorted by residual: bond pdb=" N20 T14 D1201 " pdb=" O21 T14 D1201 " ideal model delta sigma weight residual 1.347 1.204 0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" N20 T14 A1201 " pdb=" O21 T14 A1201 " ideal model delta sigma weight residual 1.347 1.205 0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" N20 T14 C1201 " pdb=" O21 T14 C1201 " ideal model delta sigma weight residual 1.347 1.205 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" N20 T14 B1201 " pdb=" O21 T14 B1201 " ideal model delta sigma weight residual 1.347 1.205 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" ND2 ASN D 821 " pdb="HD21 ASN D 821 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.66e+01 ... (remaining 56387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.78: 100798 3.78 - 7.56: 310 7.56 - 11.34: 52 11.34 - 15.12: 12 15.12 - 18.90: 12 Bond angle restraints: 101184 Sorted by residual: angle pdb=" CAT Y01 A1204 " pdb=" CBH Y01 A1204 " pdb=" CBF Y01 A1204 " ideal model delta sigma weight residual 108.46 89.56 18.90 3.00e+00 1.11e-01 3.97e+01 angle pdb=" CAT Y01 B1204 " pdb=" CBH Y01 B1204 " pdb=" CBF Y01 B1204 " ideal model delta sigma weight residual 108.46 89.57 18.89 3.00e+00 1.11e-01 3.96e+01 angle pdb=" CAT Y01 D1204 " pdb=" CBH Y01 D1204 " pdb=" CBF Y01 D1204 " ideal model delta sigma weight residual 108.46 89.59 18.87 3.00e+00 1.11e-01 3.96e+01 angle pdb=" CAT Y01 C1204 " pdb=" CBH Y01 C1204 " pdb=" CBF Y01 C1204 " ideal model delta sigma weight residual 108.46 89.59 18.87 3.00e+00 1.11e-01 3.96e+01 angle pdb=" CAT Y01 C1202 " pdb=" CBH Y01 C1202 " pdb=" CBF Y01 C1202 " ideal model delta sigma weight residual 108.46 89.81 18.65 3.00e+00 1.11e-01 3.86e+01 ... (remaining 101179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.25: 26586 29.25 - 58.51: 968 58.51 - 87.76: 36 87.76 - 117.02: 0 117.02 - 146.27: 4 Dihedral angle restraints: 27594 sinusoidal: 14266 harmonic: 13328 Sorted by residual: dihedral pdb=" CA CYS C 326 " pdb=" C CYS C 326 " pdb=" N VAL C 327 " pdb=" CA VAL C 327 " ideal model delta harmonic sigma weight residual -180.00 -150.50 -29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA CYS B 326 " pdb=" C CYS B 326 " pdb=" N VAL B 327 " pdb=" CA VAL B 327 " ideal model delta harmonic sigma weight residual -180.00 -150.51 -29.49 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA CYS A 326 " pdb=" C CYS A 326 " pdb=" N VAL A 327 " pdb=" CA VAL A 327 " ideal model delta harmonic sigma weight residual -180.00 -150.51 -29.49 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 27591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 4524 0.089 - 0.177: 152 0.177 - 0.266: 45 0.266 - 0.355: 19 0.355 - 0.443: 24 Chirality restraints: 4764 Sorted by residual: chirality pdb=" CBF Y01 C1202 " pdb=" CAS Y01 C1202 " pdb=" CBD Y01 C1202 " pdb=" CBH Y01 C1202 " both_signs ideal model delta sigma weight residual False -2.45 -2.89 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CBF Y01 A1202 " pdb=" CAS Y01 A1202 " pdb=" CBD Y01 A1202 " pdb=" CBH Y01 A1202 " both_signs ideal model delta sigma weight residual False -2.45 -2.89 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CBF Y01 D1202 " pdb=" CAS Y01 D1202 " pdb=" CBD Y01 D1202 " pdb=" CBH Y01 D1202 " both_signs ideal model delta sigma weight residual False -2.45 -2.89 0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 4761 not shown) Planarity restraints: 8544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 302 " -0.021 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" N CYS B 303 " 0.069 2.00e-02 2.50e+03 pdb=" CA CYS B 303 " -0.018 2.00e-02 2.50e+03 pdb=" H CYS B 303 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 302 " 0.021 2.00e-02 2.50e+03 3.99e-02 1.60e+01 pdb=" N CYS D 303 " -0.069 2.00e-02 2.50e+03 pdb=" CA CYS D 303 " 0.017 2.00e-02 2.50e+03 pdb=" H CYS D 303 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 302 " 0.021 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" N CYS C 303 " -0.069 2.00e-02 2.50e+03 pdb=" CA CYS C 303 " 0.017 2.00e-02 2.50e+03 pdb=" H CYS C 303 " 0.030 2.00e-02 2.50e+03 ... (remaining 8541 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 478 2.02 - 2.67: 77433 2.67 - 3.31: 159274 3.31 - 3.96: 196116 3.96 - 4.60: 313797 Nonbonded interactions: 747098 Sorted by model distance: nonbonded pdb="HH22 ARG B 829 " pdb=" OE1 GLU C 942 " model vdw 1.377 2.450 nonbonded pdb="HH22 ARG C 829 " pdb=" OE1 GLU D 942 " model vdw 1.426 2.450 nonbonded pdb=" OD2 ASP C 920 " pdb="HG21 VAL C 960 " model vdw 1.454 2.620 nonbonded pdb=" OD2 ASP A 920 " pdb="HG21 VAL A 960 " model vdw 1.454 2.620 nonbonded pdb=" OD2 ASP D 920 " pdb="HG21 VAL D 960 " model vdw 1.454 2.620 ... (remaining 747093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.790 Extract box with map and model: 1.740 Check model and map are aligned: 0.380 Set scattering table: 0.400 Process input model: 113.040 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.143 29696 Z= 0.419 Angle : 0.870 18.895 40588 Z= 0.398 Chirality : 0.054 0.443 4764 Planarity : 0.005 0.064 4944 Dihedral : 14.012 146.270 10752 Min Nonbonded Distance : 1.507 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.44 % Allowed : 12.05 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.14), residues: 3656 helix: 1.86 (0.11), residues: 2496 sheet: -0.80 (0.41), residues: 180 loop : -0.92 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 994 HIS 0.002 0.001 HIS C 500 PHE 0.013 0.001 PHE D 870 TYR 0.009 0.001 TYR C1063 ARG 0.006 0.001 ARG C 950 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 317 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 305 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 TYR cc_start: 0.7612 (m-10) cc_final: 0.6927 (m-10) REVERT: A 615 GLU cc_start: 0.8261 (tp30) cc_final: 0.8028 (tp30) REVERT: B 393 VAL cc_start: 0.9132 (p) cc_final: 0.8880 (t) REVERT: B 859 MET cc_start: 0.8677 (ttp) cc_final: 0.8386 (ttp) REVERT: C 393 VAL cc_start: 0.8972 (p) cc_final: 0.8688 (t) REVERT: C 615 GLU cc_start: 0.8257 (tp30) cc_final: 0.8035 (tp30) REVERT: C 807 PHE cc_start: 0.7876 (t80) cc_final: 0.7508 (m-10) REVERT: D 615 GLU cc_start: 0.8239 (tp30) cc_final: 0.7997 (tp30) REVERT: D 859 MET cc_start: 0.8652 (ttp) cc_final: 0.8384 (ttp) outliers start: 12 outliers final: 8 residues processed: 313 average time/residue: 1.5854 time to fit residues: 628.1704 Evaluate side-chains 256 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 248 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 316 ILE Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain D residue 137 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 2.9990 chunk 281 optimal weight: 20.0000 chunk 156 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 291 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 337 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN A 681 GLN A 934 ASN A1003 GLN B 635 ASN B 681 GLN B 914 GLN B 934 ASN B1003 GLN C 635 ASN C 681 GLN C 914 GLN C 934 ASN C1003 GLN D 635 ASN D 681 GLN D 914 GLN D 934 ASN D1003 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 29696 Z= 0.422 Angle : 0.621 5.725 40588 Z= 0.335 Chirality : 0.041 0.171 4764 Planarity : 0.005 0.054 4944 Dihedral : 8.516 59.667 5068 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.95 % Favored : 96.94 % Rotamer: Outliers : 1.49 % Allowed : 14.22 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.14), residues: 3656 helix: 1.81 (0.10), residues: 2552 sheet: -0.40 (0.39), residues: 200 loop : -1.37 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 682 HIS 0.004 0.001 HIS D 259 PHE 0.019 0.002 PHE C 870 TYR 0.014 0.002 TYR D1022 ARG 0.005 0.001 ARG A 829 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 312 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 271 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.6103 (mp10) REVERT: B 393 VAL cc_start: 0.9145 (p) cc_final: 0.8899 (t) REVERT: B 571 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.6100 (mp10) REVERT: B 859 MET cc_start: 0.8777 (ttp) cc_final: 0.8575 (ttp) REVERT: C 393 VAL cc_start: 0.9017 (p) cc_final: 0.8731 (t) REVERT: C 571 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6053 (mp10) REVERT: D 571 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6069 (mp10) outliers start: 41 outliers final: 23 residues processed: 302 average time/residue: 1.6083 time to fit residues: 611.9515 Evaluate side-chains 276 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 249 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 1022 TYR Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 137 TRP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 788 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 281 optimal weight: 20.0000 chunk 230 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 338 optimal weight: 1.9990 chunk 365 optimal weight: 0.9990 chunk 301 optimal weight: 10.0000 chunk 335 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 271 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 GLN A1003 GLN A1007 ASN B 681 GLN C 681 GLN C1003 GLN C1007 ASN D 681 GLN D1003 GLN D1007 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29696 Z= 0.348 Angle : 0.545 6.339 40588 Z= 0.298 Chirality : 0.039 0.153 4764 Planarity : 0.004 0.052 4944 Dihedral : 8.109 59.293 5064 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.97 % Favored : 95.92 % Rotamer: Outliers : 1.56 % Allowed : 15.42 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.14), residues: 3656 helix: 2.07 (0.10), residues: 2544 sheet: -0.25 (0.39), residues: 200 loop : -1.45 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 682 HIS 0.004 0.001 HIS D 946 PHE 0.017 0.002 PHE A 447 TYR 0.024 0.001 TYR A1022 ARG 0.004 0.000 ARG B 829 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 257 time to evaluate : 3.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6202 (mp10) REVERT: B 393 VAL cc_start: 0.9139 (p) cc_final: 0.8888 (t) REVERT: B 571 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6150 (mp10) REVERT: C 393 VAL cc_start: 0.9103 (p) cc_final: 0.8820 (t) REVERT: C 571 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.5838 (mp10) REVERT: C 1013 PHE cc_start: 0.8509 (t80) cc_final: 0.8289 (t80) REVERT: D 571 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.5915 (mp10) REVERT: D 1008 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6561 (mmm-85) outliers start: 43 outliers final: 16 residues processed: 297 average time/residue: 1.6367 time to fit residues: 612.0120 Evaluate side-chains 264 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 243 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 1008 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 137 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 1008 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 0.6980 chunk 254 optimal weight: 0.6980 chunk 175 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 339 optimal weight: 0.9990 chunk 359 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 321 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 681 GLN A1003 GLN A1007 ASN B 681 GLN B1003 GLN B1007 ASN C 681 GLN C 946 HIS C1003 GLN C1007 ASN D 429 GLN D 681 GLN D 946 HIS D1003 GLN D1007 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 29696 Z= 0.151 Angle : 0.472 5.414 40588 Z= 0.255 Chirality : 0.035 0.141 4764 Planarity : 0.004 0.045 4944 Dihedral : 7.483 59.856 5062 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.53 % Favored : 96.36 % Rotamer: Outliers : 1.67 % Allowed : 15.09 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.14), residues: 3656 helix: 2.43 (0.10), residues: 2540 sheet: 0.42 (0.41), residues: 172 loop : -1.26 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 994 HIS 0.002 0.001 HIS D 257 PHE 0.017 0.001 PHE B 447 TYR 0.018 0.001 TYR A1022 ARG 0.002 0.000 ARG B 842 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 304 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 258 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7973 (mm) REVERT: A 571 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.5682 (mp10) REVERT: B 393 VAL cc_start: 0.9136 (p) cc_final: 0.8902 (t) REVERT: B 488 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7985 (mm) REVERT: B 571 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.5737 (mp10) REVERT: B 615 GLU cc_start: 0.8510 (tp30) cc_final: 0.8101 (tp30) REVERT: C 393 VAL cc_start: 0.9133 (p) cc_final: 0.8865 (t) REVERT: C 453 TRP cc_start: 0.7824 (p90) cc_final: 0.7588 (p90) REVERT: C 571 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.5669 (mp10) REVERT: D 571 GLN cc_start: 0.6790 (OUTLIER) cc_final: 0.5707 (mp10) REVERT: D 1008 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6631 (mmm-85) outliers start: 46 outliers final: 19 residues processed: 299 average time/residue: 1.6532 time to fit residues: 622.4336 Evaluate side-chains 273 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 247 time to evaluate : 3.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 1056 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain B residue 1056 GLU Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 1008 ARG Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 137 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 1008 ARG Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 306 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 183 optimal weight: 20.0000 chunk 322 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 29696 Z= 0.376 Angle : 0.554 8.316 40588 Z= 0.301 Chirality : 0.039 0.152 4764 Planarity : 0.004 0.047 4944 Dihedral : 7.877 59.767 5062 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.27 % Favored : 95.62 % Rotamer: Outliers : 1.52 % Allowed : 16.33 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.14), residues: 3656 helix: 2.23 (0.10), residues: 2544 sheet: -0.17 (0.38), residues: 204 loop : -1.41 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 682 HIS 0.004 0.001 HIS D 946 PHE 0.017 0.002 PHE C 447 TYR 0.012 0.001 TYR C1022 ARG 0.003 0.000 ARG C 816 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 248 time to evaluate : 3.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7983 (mm) REVERT: A 571 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6102 (mp10) REVERT: B 393 VAL cc_start: 0.9156 (p) cc_final: 0.8915 (t) REVERT: B 488 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8001 (mm) REVERT: B 571 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.6099 (mp10) REVERT: C 393 VAL cc_start: 0.9158 (p) cc_final: 0.8891 (t) REVERT: C 571 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6005 (mp10) REVERT: C 665 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7400 (t0) REVERT: D 571 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6048 (mp10) REVERT: D 1008 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6775 (mmm-85) outliers start: 42 outliers final: 23 residues processed: 286 average time/residue: 1.6630 time to fit residues: 600.1312 Evaluate side-chains 264 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 233 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1008 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 665 ASP Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain D residue 137 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 991 ASP Chi-restraints excluded: chain D residue 1008 ARG Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 3.9990 chunk 323 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 211 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 359 optimal weight: 0.0770 chunk 298 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29696 Z= 0.259 Angle : 0.508 8.598 40588 Z= 0.276 Chirality : 0.037 0.143 4764 Planarity : 0.004 0.044 4944 Dihedral : 7.484 57.556 5062 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.86 % Favored : 96.03 % Rotamer: Outliers : 1.38 % Allowed : 16.65 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.14), residues: 3656 helix: 2.30 (0.10), residues: 2544 sheet: -0.08 (0.38), residues: 204 loop : -1.36 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 994 HIS 0.003 0.001 HIS D 946 PHE 0.016 0.001 PHE C1015 TYR 0.014 0.001 TYR C1022 ARG 0.002 0.000 ARG C 816 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 242 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7965 (mm) REVERT: A 571 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.5978 (mp10) REVERT: B 393 VAL cc_start: 0.9164 (p) cc_final: 0.8930 (t) REVERT: B 488 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7964 (mm) REVERT: B 571 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.5934 (mp10) REVERT: C 393 VAL cc_start: 0.9161 (p) cc_final: 0.8898 (t) REVERT: C 571 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.5693 (mp10) REVERT: D 571 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.5942 (mp10) REVERT: D 1008 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6764 (mmm-85) outliers start: 38 outliers final: 23 residues processed: 274 average time/residue: 1.6914 time to fit residues: 581.8461 Evaluate side-chains 270 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 3.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 137 TRP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 1008 ARG Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 137 TRP Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain C residue 137 TRP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 924 TYR Chi-restraints excluded: chain D residue 137 TRP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 1008 ARG Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 205 optimal weight: 8.9990 chunk 262 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 302 optimal weight: 0.6980 chunk 200 optimal weight: 10.0000 chunk 358 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 681 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29696 Z= 0.253 Angle : 0.500 9.569 40588 Z= 0.271 Chirality : 0.037 0.141 4764 Planarity : 0.004 0.105 4944 Dihedral : 7.201 55.403 5062 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.57 % Rotamer: Outliers : 1.63 % Allowed : 16.47 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.14), residues: 3656 helix: 2.40 (0.10), residues: 2544 sheet: -0.00 (0.39), residues: 204 loop : -1.35 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 994 HIS 0.002 0.001 HIS B 500 PHE 0.014 0.001 PHE C 870 TYR 0.013 0.001 TYR B1022 ARG 0.015 0.000 ARG C 784 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 250 time to evaluate : 3.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7909 (mm) REVERT: A 571 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.5976 (mp10) REVERT: B 393 VAL cc_start: 0.9158 (p) cc_final: 0.8957 (t) REVERT: B 488 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7914 (mm) REVERT: B 571 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.5970 (mp10) REVERT: C 393 VAL cc_start: 0.9177 (p) cc_final: 0.8938 (t) REVERT: C 571 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.5740 (mp10) REVERT: D 459 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: D 571 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.5760 (mp10) REVERT: D 1008 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6836 (mmm-85) outliers start: 45 outliers final: 19 residues processed: 286 average time/residue: 1.6016 time to fit residues: 579.9128 Evaluate side-chains 263 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 236 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 1008 ARG Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 924 TYR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 459 GLN Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 1008 ARG Chi-restraints excluded: chain D residue 1022 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 227 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 281 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29696 Z= 0.171 Angle : 0.477 12.338 40588 Z= 0.257 Chirality : 0.035 0.159 4764 Planarity : 0.004 0.055 4944 Dihedral : 6.807 55.756 5054 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.67 % Favored : 96.23 % Rotamer: Outliers : 0.91 % Allowed : 17.34 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.14), residues: 3656 helix: 2.56 (0.10), residues: 2540 sheet: 0.06 (0.39), residues: 204 loop : -1.28 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 994 HIS 0.003 0.001 HIS B 500 PHE 0.017 0.001 PHE C1015 TYR 0.071 0.001 TYR D1022 ARG 0.007 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 272 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 247 time to evaluate : 3.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 ARG cc_start: 0.8806 (tmm-80) cc_final: 0.8558 (ptm-80) REVERT: A 488 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7918 (mm) REVERT: A 571 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.5731 (mp10) REVERT: B 488 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7902 (mm) REVERT: B 571 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.5674 (mp10) REVERT: C 393 VAL cc_start: 0.9172 (p) cc_final: 0.8940 (t) REVERT: C 571 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.5666 (mp10) REVERT: D 571 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.5720 (mp10) REVERT: D 665 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7307 (t0) REVERT: D 1008 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6874 (mmm-85) outliers start: 25 outliers final: 13 residues processed: 267 average time/residue: 1.6347 time to fit residues: 548.7693 Evaluate side-chains 258 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 237 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 924 TYR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 1008 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 6.9990 chunk 343 optimal weight: 0.0470 chunk 313 optimal weight: 4.9990 chunk 334 optimal weight: 0.6980 chunk 201 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 301 optimal weight: 7.9990 chunk 316 optimal weight: 0.8980 chunk 332 optimal weight: 2.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 681 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29696 Z= 0.192 Angle : 0.476 10.592 40588 Z= 0.255 Chirality : 0.036 0.142 4764 Planarity : 0.004 0.053 4944 Dihedral : 6.689 59.139 5054 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.57 % Rotamer: Outliers : 1.09 % Allowed : 17.42 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.14), residues: 3656 helix: 2.61 (0.10), residues: 2544 sheet: 0.12 (0.39), residues: 204 loop : -1.30 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 994 HIS 0.002 0.001 HIS B 500 PHE 0.022 0.001 PHE D1015 TYR 0.018 0.001 TYR D1022 ARG 0.007 0.000 ARG C 784 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 270 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 3.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 ARG cc_start: 0.8816 (tmm-80) cc_final: 0.8556 (ptm-80) REVERT: A 571 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.5864 (mp10) REVERT: A 648 CYS cc_start: 0.5891 (m) cc_final: 0.5649 (m) REVERT: B 571 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.5871 (mp10) REVERT: B 648 CYS cc_start: 0.5820 (m) cc_final: 0.5601 (m) REVERT: B 1005 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.6838 (t80) REVERT: C 393 VAL cc_start: 0.9172 (p) cc_final: 0.8944 (t) REVERT: C 571 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.5610 (mp10) REVERT: C 648 CYS cc_start: 0.5631 (m) cc_final: 0.5374 (m) REVERT: C 1059 MET cc_start: 0.8370 (mmm) cc_final: 0.8170 (mmm) REVERT: D 571 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.5639 (mp10) REVERT: D 645 VAL cc_start: 0.8794 (t) cc_final: 0.8437 (m) REVERT: D 648 CYS cc_start: 0.5908 (m) cc_final: 0.5689 (m) REVERT: D 665 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7316 (t0) REVERT: D 1008 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6881 (mmm-85) outliers start: 30 outliers final: 13 residues processed: 262 average time/residue: 1.6088 time to fit residues: 531.7196 Evaluate side-chains 254 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 234 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 924 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 665 ASP Chi-restraints excluded: chain D residue 1008 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 3.9990 chunk 353 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 370 optimal weight: 7.9990 chunk 341 optimal weight: 2.9990 chunk 295 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1003 GLN D1007 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 29696 Z= 0.395 Angle : 0.561 14.467 40588 Z= 0.303 Chirality : 0.039 0.162 4764 Planarity : 0.004 0.048 4944 Dihedral : 7.252 56.629 5054 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.43 % Favored : 95.43 % Rotamer: Outliers : 0.91 % Allowed : 17.74 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.14), residues: 3656 helix: 2.34 (0.10), residues: 2544 sheet: -0.10 (0.38), residues: 212 loop : -1.46 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 682 HIS 0.003 0.001 HIS D 928 PHE 0.017 0.002 PHE D 870 TYR 0.012 0.001 TYR B1022 ARG 0.007 0.001 ARG B 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Residue LEU 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue LYS 50 is missing expected H atoms. Skipping. Residue LYS 116 is missing expected H atoms. Skipping. Residue TYR 117 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 153 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue MET 219 is missing expected H atoms. Skipping. Residue LEU 226 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue MET 242 is missing expected H atoms. Skipping. Residue LEU 250 is missing expected H atoms. Skipping. Residue THR 289 is missing expected H atoms. Skipping. Residue SER 293 is missing expected H atoms. Skipping. Residue SER 332 is missing expected H atoms. Skipping. Residue THR 365 is missing expected H atoms. Skipping. Residue LEU 369 is missing expected H atoms. Skipping. Residue LYS 382 is missing expected H atoms. Skipping. Residue LEU 385 is missing expected H atoms. Skipping. Residue LYS 395 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue LYS 423 is missing expected H atoms. Skipping. Residue SER 455 is missing expected H atoms. Skipping. Residue LYS 468 is missing expected H atoms. Skipping. Residue LYS 486 is missing expected H atoms. Skipping. Residue THR 489 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue ILE 511 is missing expected H atoms. Skipping. Residue LYS 513 is missing expected H atoms. Skipping. Residue THR 522 is missing expected H atoms. Skipping. Residue LYS 526 is missing expected H atoms. Skipping. Residue SER 534 is missing expected H atoms. Skipping. Residue LYS 585 is missing expected H atoms. Skipping. Residue LYS 603 is missing expected H atoms. Skipping. Residue LYS 605 is missing expected H atoms. Skipping. Residue LYS 715 is missing expected H atoms. Skipping. Residue LEU 723 is missing expected H atoms. Skipping. Residue SER 917 is missing expected H atoms. Skipping. Residue VAL 919 is missing expected H atoms. Skipping. Residue VAL 1025 is missing expected H atoms. Skipping. Residue LYS 1027 is missing expected H atoms. Skipping. Residue LYS 1070 is missing expected H atoms. Skipping. Residue SER 1075 is missing expected H atoms. Skipping. Residue MET 1078 is missing expected H atoms. Skipping. Residue LEU 1085 is missing expected H atoms. Skipping. Residue LYS 1088 is missing expected H atoms. Skipping. Residue LEU 1089 is missing expected H atoms. Skipping. Residue LEU 1092 is missing expected H atoms. Skipping. Residue LYS 1093 is missing expected H atoms. Skipping. Residue LEU 1095 is missing expected H atoms. Skipping. Residue LEU 1096 is missing expected H atoms. Skipping. Residue LYS 1097 is missing expected H atoms. Skipping. Residue ILE 1099 is missing expected H atoms. Skipping. Residue ILE 1103 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 241 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.6095 (mp10) REVERT: B 571 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6087 (mp10) REVERT: C 393 VAL cc_start: 0.9174 (p) cc_final: 0.8968 (t) REVERT: C 571 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6003 (mp10) REVERT: D 571 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6036 (mp10) REVERT: D 784 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7539 (ttp80) REVERT: D 1008 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6951 (mmm-85) outliers start: 25 outliers final: 20 residues processed: 258 average time/residue: 1.7421 time to fit residues: 560.8150 Evaluate side-chains 260 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 3.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 571 GLN Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1005 TYR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 429 GLN Chi-restraints excluded: chain C residue 571 GLN Chi-restraints excluded: chain C residue 924 TYR Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1008 ARG Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 784 ARG Chi-restraints excluded: chain D residue 991 ASP Chi-restraints excluded: chain D residue 1008 ARG Chi-restraints excluded: chain D residue 1022 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 chunk 272 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 295 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 303 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.144189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.086123 restraints weight = 128049.553| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.16 r_work: 0.3054 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 29696 Z= 0.272 Angle : 0.532 14.678 40588 Z= 0.285 Chirality : 0.037 0.240 4764 Planarity : 0.004 0.047 4944 Dihedral : 7.005 55.634 5054 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.35 % Favored : 95.54 % Rotamer: Outliers : 1.05 % Allowed : 17.71 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.14), residues: 3656 helix: 2.38 (0.10), residues: 2544 sheet: -0.09 (0.38), residues: 212 loop : -1.40 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 994 HIS 0.002 0.001 HIS D 928 PHE 0.020 0.001 PHE C1015 TYR 0.087 0.001 TYR D1022 ARG 0.006 0.000 ARG B 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12690.57 seconds wall clock time: 218 minutes 38.48 seconds (13118.48 seconds total)