Starting phenix.real_space_refine on Mon Feb 19 04:21:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/02_2024/8f4r_28857_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/02_2024/8f4r_28857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/02_2024/8f4r_28857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/02_2024/8f4r_28857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/02_2024/8f4r_28857_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f4r_28857/02_2024/8f4r_28857_updated.pdb" } resolution = 3.06 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= 0.000 sd= 0.047 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: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 15122 2.51 5 N 3992 2.21 5 O 4429 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23675 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 7865 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 989} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 7898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7898 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 991} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 7881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 7881 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 991} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LLL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.59, per 1000 atoms: 0.53 Number of scatterers: 23675 At special positions: 0 Unit cell: (124.12, 114.49, 141.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4429 8.00 N 3992 7.00 C 15122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 10.05 Conformation dependent library (CDL) restraints added in 4.4 seconds 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 109 helices and 27 sheets defined 54.3% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.31 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.523A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 113 removed outlier: 3.962A pdb=" N SER A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.769A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 200 through 210 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 299 through 316 removed outlier: 3.885A pdb=" N GLN A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 358 Processing helix chain 'A' and resid 362 through 385 Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 392 through 423 removed outlier: 4.160A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 437 Processing helix chain 'A' and resid 439 through 458 Proline residue: A 455 - end of helix removed outlier: 4.144A pdb=" N PHE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 496 removed outlier: 4.554A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 501 through 506 Processing helix chain 'A' and resid 511 through 535 Processing helix chain 'A' and resid 537 through 557 Processing helix chain 'A' and resid 583 through 600 Processing helix chain 'A' and resid 643 through 655 Processing helix chain 'A' and resid 691 through 707 removed outlier: 3.683A pdb=" N GLU A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 741 through 751 Processing helix chain 'A' and resid 775 through 777 No H-bonds generated for 'chain 'A' and resid 775 through 777' Processing helix chain 'A' and resid 781 through 786 Processing helix chain 'A' and resid 799 through 802 No H-bonds generated for 'chain 'A' and resid 799 through 802' Processing helix chain 'A' and resid 835 through 848 Processing helix chain 'A' and resid 860 through 866 Processing helix chain 'A' and resid 870 through 890 Processing helix chain 'A' and resid 895 through 916 removed outlier: 3.830A pdb=" N VAL A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Proline residue: A 904 - end of helix removed outlier: 3.506A pdb=" N VAL A 907 " --> pdb=" O VAL A 903 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLY A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 910 " --> pdb=" O GLY A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 952 Processing helix chain 'A' and resid 957 through 987 removed outlier: 4.549A pdb=" N ARG A 970 " --> pdb=" O ARG A 966 " (cutoff:3.500A) Proline residue: A 971 - end of helix Proline residue: A 985 - end of helix Processing helix chain 'A' and resid 994 through 1029 removed outlier: 4.271A pdb=" N TYR A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Proline residue: A1020 - end of helix Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.539A pdb=" N PHE B 28 " --> pdb=" O THR B 24 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 62 through 69 removed outlier: 4.056A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 113 removed outlier: 3.627A pdb=" N GLN B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 243 through 247 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 299 through 316 removed outlier: 3.702A pdb=" N GLN B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 358 Processing helix chain 'B' and resid 362 through 385 removed outlier: 3.747A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix removed outlier: 3.662A pdb=" N VAL B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 392 through 423 removed outlier: 3.507A pdb=" N ILE B 402 " --> pdb=" O MET B 398 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 458 removed outlier: 3.917A pdb=" N GLY B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLY B 440 " --> pdb=" O GLY B 436 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 4.045A pdb=" N PHE B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 486 Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 510 through 534 removed outlier: 3.775A pdb=" N TRP B 514 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE B 515 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 534 " --> pdb=" O ALA B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 556 Processing helix chain 'B' and resid 583 through 599 Processing helix chain 'B' and resid 643 through 656 removed outlier: 4.050A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 707 Processing helix chain 'B' and resid 731 through 737 Processing helix chain 'B' and resid 741 through 752 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 781 through 786 removed outlier: 3.683A pdb=" N ILE B 784 " --> pdb=" O PRO B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 801 No H-bonds generated for 'chain 'B' and resid 799 through 801' Processing helix chain 'B' and resid 835 through 848 removed outlier: 3.571A pdb=" N LYS B 847 " --> pdb=" O GLU B 843 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN B 848 " --> pdb=" O SER B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 890 Proline residue: B 872 - end of helix Processing helix chain 'B' and resid 895 through 917 removed outlier: 4.286A pdb=" N VAL B 902 " --> pdb=" O SER B 898 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL B 903 " --> pdb=" O VAL B 899 " (cutoff:3.500A) Proline residue: B 904 - end of helix removed outlier: 3.986A pdb=" N GLY B 909 " --> pdb=" O LEU B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 953 removed outlier: 4.564A pdb=" N PHE B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 967 Processing helix chain 'B' and resid 969 through 987 Proline residue: B 985 - end of helix Processing helix chain 'B' and resid 994 through 1013 removed outlier: 4.365A pdb=" N GLY B1003 " --> pdb=" O ALA B 999 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL B1004 " --> pdb=" O VAL B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1029 Proline residue: B1020 - end of helix Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 9 through 29 Processing helix chain 'C' and resid 54 through 60 Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.527A pdb=" N ASN C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 117 removed outlier: 4.139A pdb=" N SER C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA C 114 " --> pdb=" O GLN C 110 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ARG C 116 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LYS C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 163 through 168 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 200 through 210 Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 299 through 316 removed outlier: 4.549A pdb=" N TYR C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 359 Processing helix chain 'C' and resid 362 through 386 removed outlier: 3.843A pdb=" N ILE C 367 " --> pdb=" O ARG C 363 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.569A pdb=" N ALA C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 372 " --> pdb=" O PRO C 368 " (cutoff:3.500A) Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 392 through 400 Processing helix chain 'C' and resid 402 through 422 removed outlier: 4.176A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 458 removed outlier: 5.757A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Proline residue: C 455 - end of helix removed outlier: 3.988A pdb=" N PHE C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 495 removed outlier: 4.593A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 512 through 533 removed outlier: 4.242A pdb=" N ILE C 533 " --> pdb=" O GLY C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 557 Processing helix chain 'C' and resid 583 through 599 Processing helix chain 'C' and resid 643 through 656 Processing helix chain 'C' and resid 691 through 707 Processing helix chain 'C' and resid 731 through 736 Processing helix chain 'C' and resid 741 through 751 Processing helix chain 'C' and resid 775 through 777 No H-bonds generated for 'chain 'C' and resid 775 through 777' Processing helix chain 'C' and resid 781 through 786 Processing helix chain 'C' and resid 799 through 801 No H-bonds generated for 'chain 'C' and resid 799 through 801' Processing helix chain 'C' and resid 835 through 848 Processing helix chain 'C' and resid 860 through 866 Processing helix chain 'C' and resid 871 through 890 Processing helix chain 'C' and resid 895 through 916 removed outlier: 4.457A pdb=" N VAL C 902 " --> pdb=" O SER C 898 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL C 903 " --> pdb=" O VAL C 899 " (cutoff:3.500A) Proline residue: C 904 - end of helix removed outlier: 3.998A pdb=" N GLY C 909 " --> pdb=" O LEU C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 953 removed outlier: 3.752A pdb=" N ILE C 943 " --> pdb=" O ASN C 939 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 987 removed outlier: 4.867A pdb=" N ARG C 970 " --> pdb=" O ARG C 966 " (cutoff:3.500A) Proline residue: C 971 - end of helix Proline residue: C 985 - end of helix Processing helix chain 'C' and resid 994 through 1029 removed outlier: 4.314A pdb=" N GLY C1003 " --> pdb=" O ALA C 999 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C1016 " --> pdb=" O THR C1012 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Proline residue: C1020 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.718A pdb=" N ASN A 42 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 77 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 321 through 325 removed outlier: 6.957A pdb=" N VAL A 291 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR A 139 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU A 289 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA A 141 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER A 287 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASP A 174 " --> pdb=" O LYS A 292 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.162A pdb=" N VAL A 766 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N MET A 184 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A 768 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE A 186 " --> pdb=" O LYS A 768 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR A 770 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU A 188 " --> pdb=" O TYR A 770 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLN A 772 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN A 758 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL A 771 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR A 756 " --> pdb=" O VAL A 771 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 278 through 281 removed outlier: 6.731A pdb=" N ARG A 629 " --> pdb=" O MET A 606 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL A 608 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE A 627 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA A 610 " --> pdb=" O ARG A 625 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG A 625 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL A 612 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL A 623 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 822 through 828 removed outlier: 4.294A pdb=" N ASP A 680 " --> pdb=" O THR A 858 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 721 through 729 Processing sheet with id= G, first strand: chain 'A' and resid 788 through 790 Processing sheet with id= H, first strand: chain 'A' and resid 215 through 218 removed outlier: 6.860A pdb=" N ILE A 234 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.798A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 127 through 131 removed outlier: 3.540A pdb=" N TYR B 77 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 321 through 325 removed outlier: 6.895A pdb=" N VAL B 291 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR B 139 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU B 289 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA B 141 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER B 287 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.386A pdb=" N TYR B 182 " --> pdb=" O VAL B 766 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS B 768 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN B 758 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B 771 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N TYR B 756 " --> pdb=" O VAL B 771 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 217 through 219 removed outlier: 4.128A pdb=" N GLY B 217 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 284 through 286 removed outlier: 4.251A pdb=" N SER B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG B 629 " --> pdb=" O MET B 606 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL B 608 " --> pdb=" O PHE B 627 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE B 627 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA B 610 " --> pdb=" O ARG B 625 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG B 625 " --> pdb=" O ALA B 610 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL B 612 " --> pdb=" O VAL B 623 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N VAL B 623 " --> pdb=" O VAL B 612 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 822 through 826 Processing sheet with id= P, first strand: chain 'B' and resid 721 through 729 Processing sheet with id= Q, first strand: chain 'B' and resid 788 through 790 Processing sheet with id= R, first strand: chain 'B' and resid 250 through 253 removed outlier: 6.841A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.024A pdb=" N GLN C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 266 through 272 Processing sheet with id= U, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.290A pdb=" N SER C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG C 629 " --> pdb=" O MET C 606 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL C 608 " --> pdb=" O PHE C 627 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE C 627 " --> pdb=" O VAL C 608 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA C 610 " --> pdb=" O ARG C 625 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG C 625 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N VAL C 612 " --> pdb=" O VAL C 623 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL C 623 " --> pdb=" O VAL C 612 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 822 through 826 Processing sheet with id= W, first strand: chain 'C' and resid 721 through 729 Processing sheet with id= X, first strand: chain 'C' and resid 759 through 762 Processing sheet with id= Y, first strand: chain 'C' and resid 788 through 790 Processing sheet with id= Z, first strand: chain 'C' and resid 321 through 328 removed outlier: 6.476A pdb=" N THR C 139 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU C 328 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ILE C 137 " --> pdb=" O GLU C 328 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL C 291 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR C 139 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU C 289 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA C 141 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER C 287 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 250 through 253 removed outlier: 6.657A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) 1350 hydrogen bonds defined for protein. 3936 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: 9.54 Time building geometry restraints manager: 10.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7775 1.34 - 1.46: 3862 1.46 - 1.57: 12240 1.57 - 1.69: 5 1.69 - 1.81: 252 Bond restraints: 24134 Sorted by residual: bond pdb=" C51 LLL B1101 " pdb=" C61 LLL B1101 " ideal model delta sigma weight residual 1.515 1.590 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C42 LLL B1101 " pdb=" C52 LLL B1101 " ideal model delta sigma weight residual 1.529 1.601 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" CA PHE A1030 " pdb=" C PHE A1030 " ideal model delta sigma weight residual 1.532 1.511 0.022 6.50e-03 2.37e+04 1.10e+01 bond pdb=" C32 LLL B1101 " pdb=" C42 LLL B1101 " ideal model delta sigma weight residual 1.529 1.592 -0.063 2.00e-02 2.50e+03 9.93e+00 bond pdb=" C33 LLL B1101 " pdb=" C43 LLL B1101 " ideal model delta sigma weight residual 1.541 1.603 -0.062 2.00e-02 2.50e+03 9.61e+00 ... (remaining 24129 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.65: 690 106.65 - 113.49: 13429 113.49 - 120.33: 8414 120.33 - 127.17: 10049 127.17 - 134.00: 218 Bond angle restraints: 32800 Sorted by residual: angle pdb=" C ALA B 859 " pdb=" CA ALA B 859 " pdb=" CB ALA B 859 " ideal model delta sigma weight residual 116.54 110.06 6.48 1.15e+00 7.56e-01 3.18e+01 angle pdb=" C LEU B 500 " pdb=" CA LEU B 500 " pdb=" CB LEU B 500 " ideal model delta sigma weight residual 117.23 110.78 6.45 1.36e+00 5.41e-01 2.25e+01 angle pdb=" C ASN C 818 " pdb=" CA ASN C 818 " pdb=" CB ASN C 818 " ideal model delta sigma weight residual 116.54 111.21 5.33 1.15e+00 7.56e-01 2.15e+01 angle pdb=" C SER C 894 " pdb=" N VAL C 895 " pdb=" CA VAL C 895 " ideal model delta sigma weight residual 120.24 122.84 -2.60 6.30e-01 2.52e+00 1.70e+01 angle pdb=" CA ALA B 859 " pdb=" C ALA B 859 " pdb=" N MET B 860 " ideal model delta sigma weight residual 119.52 116.45 3.07 7.90e-01 1.60e+00 1.51e+01 ... (remaining 32795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.83: 14095 25.83 - 51.66: 301 51.66 - 77.48: 35 77.48 - 103.31: 7 103.31 - 129.14: 8 Dihedral angle restraints: 14446 sinusoidal: 5554 harmonic: 8892 Sorted by residual: dihedral pdb=" O23 LLL B1101 " pdb=" C13 LLL B1101 " pdb=" C23 LLL B1101 " pdb=" O53 LLL B1101 " ideal model delta sinusoidal sigma weight residual 178.81 -52.05 -129.14 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C11 LLL B1101 " pdb=" C51 LLL B1101 " pdb=" O51 LLL B1101 " pdb=" C61 LLL B1101 " ideal model delta sinusoidal sigma weight residual 174.24 -57.43 -128.33 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C11 LLL B1101 " pdb=" C51 LLL B1101 " pdb=" O51 LLL B1101 " pdb=" C41 LLL B1101 " ideal model delta sinusoidal sigma weight residual -60.30 64.56 -124.86 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 14443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3811 0.134 - 0.269: 5 0.269 - 0.403: 4 0.403 - 0.537: 1 0.537 - 0.671: 3 Chirality restraints: 3824 Sorted by residual: chirality pdb=" C62 LLL B1101 " pdb=" C12 LLL B1101 " pdb=" C52 LLL B1101 " pdb=" O62 LLL B1101 " both_signs ideal model delta sigma weight residual False -2.49 -3.16 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" C42 LLL B1101 " pdb=" C32 LLL B1101 " pdb=" C52 LLL B1101 " pdb=" O11 LLL B1101 " both_signs ideal model delta sigma weight residual False 2.54 3.21 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" C52 LLL B1101 " pdb=" C42 LLL B1101 " pdb=" C62 LLL B1101 " pdb=" O52 LLL B1101 " both_signs ideal model delta sigma weight residual False -2.47 -3.05 0.58 2.00e-01 2.50e+01 8.38e+00 ... (remaining 3821 not shown) Planarity restraints: 4225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 871 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO C 872 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 872 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 872 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 426 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.81e+00 pdb=" N PRO A 427 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 830 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 831 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 831 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 831 " -0.017 5.00e-02 4.00e+02 ... (remaining 4222 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3475 2.75 - 3.29: 24244 3.29 - 3.82: 40777 3.82 - 4.36: 47709 4.36 - 4.90: 83622 Nonbonded interactions: 199827 Sorted by model distance: nonbonded pdb=" O ALA A 451 " pdb=" OG SER A 878 " model vdw 2.212 2.440 nonbonded pdb=" OH TYR A 526 " pdb=" O ILE A1016 " model vdw 2.222 2.440 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 759 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR C 526 " pdb=" O ILE C1016 " model vdw 2.232 2.440 nonbonded pdb=" OD1 ASP B 153 " pdb=" OH TYR B 182 " model vdw 2.276 2.440 ... (remaining 199822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 94 or (resid 95 through 96 and (name N or name C \ A or name C or name O or name CB )) or resid 97 through 432 or (resid 433 and (n \ ame N or name CA or name C or name O or name CB )) or resid 434 through 505 or ( \ resid 506 and (name N or name CA or name C or name O or name CB )) or (resid 507 \ through 509 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 10 through 1031)) selection = (chain 'B' and (resid 1 through 94 or (resid 95 through 96 and (name N or name C \ A or name C or name O or name CB )) or resid 97 through 432 or (resid 433 and (n \ ame N or name CA or name C or name O or name CB )) or resid 434 through 499 or ( \ resid 500 through 502 and (name N or name CA or name C or name O or name CB )) o \ r (resid 503 through 506 and (name N or name CA or name C or name O or name CB ) \ ) or resid 507 or (resid 508 through 509 and (name N or name CA or name C or nam \ e O or name CB )) or resid 510 through 638 or (resid 639 and (name N or name CA \ or name C or name O or name CB )) or resid 640 through 657 or (resid 658 and (na \ me N or name CA or name C or name O or name CB )) or resid 659 through 1031)) selection = (chain 'C' and (resid 1 through 499 or (resid 500 through 502 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 503 through 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 or (resid 508 through 509 \ and (name N or name CA or name C or name O or name CB )) or resid 510 through 6 \ 57 or (resid 658 and (name N or name CA or name C or name O or name CB )) or res \ id 659 through 1031)) } 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: 2.570 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: 0.020 Extract box with map and model: 10.850 Check model and map are aligned: 0.350 Set scattering table: 0.250 Process input model: 66.410 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.090 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 0.004 0.075 24134 Z= 0.279 Angle : 0.561 10.117 32800 Z= 0.324 Chirality : 0.044 0.671 3824 Planarity : 0.003 0.038 4225 Dihedral : 11.500 129.138 8738 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.23 % Favored : 98.74 % Rotamer: Outliers : 3.22 % Allowed : 5.53 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.85 (0.15), residues: 3091 helix: 2.32 (0.12), residues: 1691 sheet: -0.26 (0.26), residues: 427 loop : 0.04 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 540 HIS 0.005 0.001 HIS A 506 PHE 0.010 0.001 PHE C 571 TYR 0.010 0.001 TYR C 862 ARG 0.005 0.000 ARG B 813 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 640 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 ASN cc_start: 0.7791 (m110) cc_final: 0.7572 (m110) REVERT: A 799 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8421 (t80) REVERT: B 135 THR cc_start: 0.7241 (p) cc_final: 0.6754 (p) REVERT: B 682 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7134 (tp30) REVERT: B 726 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7497 (tp40) REVERT: B 880 LEU cc_start: 0.8478 (tp) cc_final: 0.8232 (tp) REVERT: C 270 MET cc_start: 0.8061 (ttp) cc_final: 0.7677 (ttp) REVERT: C 683 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8233 (tp) REVERT: C 731 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6050 (mp10) REVERT: C 777 TYR cc_start: 0.8573 (m-80) cc_final: 0.8260 (m-80) outliers start: 81 outliers final: 25 residues processed: 696 average time/residue: 0.3667 time to fit residues: 394.5812 Evaluate side-chains 420 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 390 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 726 GLN Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 731 GLN Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 833 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 2.9990 chunk 234 optimal weight: 0.0570 chunk 129 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 180 optimal weight: 0.7980 chunk 280 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 59 ASN A 81 GLN A 87 GLN A 105 GLN ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 ASN A 213 GLN A 237 GLN A 437 GLN A 439 GLN A 469 GLN A 517 GLN A 583 GLN A 585 GLN A 592 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 GLN ** A 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 109 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 213 GLN B 255 GLN B 592 GLN B 621 GLN B 700 GLN B 708 ASN B 724 GLN B 726 GLN B 749 GLN B 818 ASN B 926 GLN C 87 GLN C 110 GLN C 120 GLN C 123 GLN C 124 ASN C 241 GLN C 254 ASN C 415 ASN C 576 GLN C 584 GLN C 655 ASN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 HIS C 700 GLN ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 ASN C 749 GLN C 863 GLN C 967 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24134 Z= 0.179 Angle : 0.508 7.904 32800 Z= 0.259 Chirality : 0.039 0.238 3824 Planarity : 0.004 0.034 4225 Dihedral : 7.782 101.583 3443 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.00 % Favored : 98.96 % Rotamer: Outliers : 3.50 % Allowed : 9.71 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.95 (0.15), residues: 3091 helix: 2.36 (0.12), residues: 1699 sheet: -0.21 (0.25), residues: 448 loop : 0.15 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 540 HIS 0.005 0.001 HIS A 506 PHE 0.021 0.001 PHE C 511 TYR 0.015 0.001 TYR B 467 ARG 0.005 0.000 ARG B 813 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 429 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 799 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8338 (t80) REVERT: B 135 THR cc_start: 0.6966 (p) cc_final: 0.6619 (p) REVERT: B 168 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.6833 (mpp-170) REVERT: B 682 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7154 (tp30) REVERT: C 270 MET cc_start: 0.7895 (ttp) cc_final: 0.7458 (ttp) REVERT: C 731 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.5926 (mp10) REVERT: C 777 TYR cc_start: 0.8487 (m-80) cc_final: 0.8196 (m-80) outliers start: 88 outliers final: 51 residues processed: 487 average time/residue: 0.3456 time to fit residues: 269.1973 Evaluate side-chains 423 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 368 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 682 GLU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 728 ASP Chi-restraints excluded: chain C residue 731 GLN Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 932 VAL Chi-restraints excluded: chain C residue 944 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 77 optimal weight: 0.0570 chunk 281 optimal weight: 2.9990 chunk 303 optimal weight: 0.5980 chunk 250 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 225 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 GLN A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 HIS C 716 HIS ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 951 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24134 Z= 0.168 Angle : 0.491 8.846 32800 Z= 0.247 Chirality : 0.038 0.282 3824 Planarity : 0.003 0.035 4225 Dihedral : 6.559 86.624 3427 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.10 % Favored : 98.87 % Rotamer: Outliers : 3.70 % Allowed : 11.66 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.92 (0.15), residues: 3091 helix: 2.33 (0.12), residues: 1697 sheet: -0.25 (0.25), residues: 441 loop : 0.17 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 540 HIS 0.005 0.001 HIS A 506 PHE 0.018 0.001 PHE C 511 TYR 0.010 0.001 TYR B 467 ARG 0.005 0.000 ARG A 813 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 399 time to evaluate : 2.666 Fit side-chains revert: symmetry clash REVERT: A 182 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: A 439 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6708 (mt0) REVERT: A 799 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8336 (t80) REVERT: B 135 THR cc_start: 0.7012 (p) cc_final: 0.6655 (p) REVERT: B 168 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.6857 (mtp180) REVERT: C 270 MET cc_start: 0.7879 (ttp) cc_final: 0.7481 (ttp) REVERT: C 731 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.5934 (mp10) REVERT: C 777 TYR cc_start: 0.8483 (m-80) cc_final: 0.8175 (m-80) outliers start: 93 outliers final: 53 residues processed: 462 average time/residue: 0.3622 time to fit residues: 270.4872 Evaluate side-chains 418 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 360 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 439 GLN Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 731 GLN Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 944 VAL Chi-restraints excluded: chain C residue 1009 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.5980 chunk 211 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 134 optimal weight: 0.1980 chunk 188 optimal weight: 0.6980 chunk 282 optimal weight: 2.9990 chunk 298 optimal weight: 7.9990 chunk 147 optimal weight: 0.7980 chunk 267 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 124 ASN C 360 GLN ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24134 Z= 0.161 Angle : 0.474 8.465 32800 Z= 0.238 Chirality : 0.038 0.328 3824 Planarity : 0.003 0.035 4225 Dihedral : 5.879 73.319 3419 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 0.94 % Favored : 99.03 % Rotamer: Outliers : 3.98 % Allowed : 11.86 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.94 (0.15), residues: 3091 helix: 2.33 (0.12), residues: 1693 sheet: -0.16 (0.25), residues: 433 loop : 0.18 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 540 HIS 0.005 0.001 HIS A 506 PHE 0.016 0.001 PHE C 511 TYR 0.009 0.001 TYR B 467 ARG 0.004 0.000 ARG A 813 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 386 time to evaluate : 2.652 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7323 (pp) REVERT: A 182 TYR cc_start: 0.8569 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: A 799 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8341 (t80) REVERT: B 135 THR cc_start: 0.6998 (p) cc_final: 0.6677 (p) REVERT: B 168 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.6836 (mtp180) REVERT: C 731 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.5940 (mp10) REVERT: C 777 TYR cc_start: 0.8488 (m-80) cc_final: 0.8149 (m-80) outliers start: 100 outliers final: 63 residues processed: 453 average time/residue: 0.3209 time to fit residues: 233.5467 Evaluate side-chains 425 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 357 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 731 GLN Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 932 VAL Chi-restraints excluded: chain C residue 1009 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 222 optimal weight: 0.0870 chunk 123 optimal weight: 0.5980 chunk 254 optimal weight: 1.9990 chunk 206 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 268 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN B 237 GLN B 716 HIS B 870 GLN C 120 GLN C 124 ASN C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24134 Z= 0.172 Angle : 0.474 9.371 32800 Z= 0.239 Chirality : 0.038 0.328 3824 Planarity : 0.003 0.035 4225 Dihedral : 5.623 62.938 3416 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.07 % Favored : 98.90 % Rotamer: Outliers : 4.10 % Allowed : 12.18 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.95 (0.15), residues: 3091 helix: 2.33 (0.13), residues: 1697 sheet: -0.09 (0.25), residues: 431 loop : 0.17 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 540 HIS 0.005 0.001 HIS A 506 PHE 0.015 0.001 PHE C 511 TYR 0.009 0.001 TYR C 862 ARG 0.006 0.000 ARG B 813 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 377 time to evaluate : 2.812 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7326 (pt) REVERT: A 182 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7602 (m-80) REVERT: A 799 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8360 (t80) REVERT: B 135 THR cc_start: 0.7025 (p) cc_final: 0.6702 (p) REVERT: B 168 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6845 (mtp180) REVERT: B 710 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6379 (mt-10) REVERT: C 777 TYR cc_start: 0.8444 (m-80) cc_final: 0.8127 (m-80) outliers start: 103 outliers final: 68 residues processed: 442 average time/residue: 0.3446 time to fit residues: 242.9670 Evaluate side-chains 425 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 352 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 922 ASP Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 680 ASP Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 932 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1009 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 439 GLN A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 GLN B 81 GLN B 254 ASN C 112 GLN C 120 GLN C 124 ASN C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24134 Z= 0.199 Angle : 0.487 10.277 32800 Z= 0.244 Chirality : 0.039 0.325 3824 Planarity : 0.003 0.036 4225 Dihedral : 5.384 59.155 3413 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.80 % Rotamer: Outliers : 4.06 % Allowed : 12.57 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 (0.15), residues: 3091 helix: 2.32 (0.13), residues: 1696 sheet: -0.07 (0.25), residues: 434 loop : 0.18 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 540 HIS 0.005 0.001 HIS A 506 PHE 0.018 0.001 PHE C 511 TYR 0.008 0.001 TYR B 467 ARG 0.005 0.000 ARG B1028 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 366 time to evaluate : 2.852 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7479 (pt) REVERT: A 182 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: A 799 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8355 (t80) REVERT: B 135 THR cc_start: 0.7036 (p) cc_final: 0.6731 (p) REVERT: B 168 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6848 (mtp180) REVERT: B 710 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6392 (mt-10) REVERT: C 777 TYR cc_start: 0.8456 (m-80) cc_final: 0.8176 (m-80) outliers start: 102 outliers final: 70 residues processed: 431 average time/residue: 0.3643 time to fit residues: 250.9613 Evaluate side-chains 424 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 349 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 845 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 932 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1009 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 218 optimal weight: 6.9990 chunk 169 optimal weight: 0.0020 chunk 251 optimal weight: 0.8980 chunk 166 optimal weight: 0.0070 chunk 297 optimal weight: 0.2980 chunk 186 optimal weight: 3.9990 chunk 181 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 overall best weight: 0.3206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 ASN B 81 GLN C 120 GLN C 124 ASN C 254 ASN C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24134 Z= 0.135 Angle : 0.469 10.570 32800 Z= 0.234 Chirality : 0.037 0.289 3824 Planarity : 0.003 0.037 4225 Dihedral : 5.127 59.406 3413 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.10 % Favored : 98.87 % Rotamer: Outliers : 2.98 % Allowed : 13.89 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 2.06 (0.15), residues: 3091 helix: 2.37 (0.13), residues: 1696 sheet: 0.16 (0.25), residues: 425 loop : 0.20 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 540 HIS 0.005 0.001 HIS A 506 PHE 0.016 0.001 PHE C 511 TYR 0.011 0.001 TYR A 327 ARG 0.005 0.000 ARG A1028 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 392 time to evaluate : 2.896 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7340 (pt) REVERT: A 182 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7556 (m-80) REVERT: A 656 GLN cc_start: 0.6952 (mm110) cc_final: 0.6734 (mm-40) REVERT: A 799 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8338 (t80) REVERT: B 135 THR cc_start: 0.7044 (p) cc_final: 0.6734 (p) REVERT: B 168 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6824 (mtp180) REVERT: B 710 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6254 (mt-10) outliers start: 75 outliers final: 51 residues processed: 447 average time/residue: 0.3234 time to fit residues: 232.3326 Evaluate side-chains 412 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 356 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 1009 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 chunk 202 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 234 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 HIS A 517 GLN A 749 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 124 ASN C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 24134 Z= 0.177 Angle : 0.484 10.461 32800 Z= 0.242 Chirality : 0.038 0.258 3824 Planarity : 0.003 0.036 4225 Dihedral : 4.840 59.822 3409 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.80 % Rotamer: Outliers : 2.90 % Allowed : 14.64 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 2.02 (0.15), residues: 3091 helix: 2.34 (0.13), residues: 1696 sheet: 0.08 (0.25), residues: 447 loop : 0.20 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 540 HIS 0.005 0.001 HIS A 506 PHE 0.016 0.001 PHE C 511 TYR 0.011 0.001 TYR A 327 ARG 0.003 0.000 ARG A1028 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 357 time to evaluate : 2.819 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7340 (pt) REVERT: A 182 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: A 656 GLN cc_start: 0.6923 (mm110) cc_final: 0.6719 (mm-40) REVERT: A 799 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8376 (t80) REVERT: B 135 THR cc_start: 0.7105 (p) cc_final: 0.6776 (p) REVERT: B 168 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6778 (mtp180) REVERT: B 710 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6290 (mt-10) outliers start: 73 outliers final: 57 residues processed: 405 average time/residue: 0.3336 time to fit residues: 218.0262 Evaluate side-chains 410 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 348 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 902 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1009 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 4.9990 chunk 285 optimal weight: 1.9990 chunk 260 optimal weight: 5.9990 chunk 277 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 250 optimal weight: 0.2980 chunk 262 optimal weight: 3.9990 chunk 276 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A 749 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN C 120 GLN C 124 ASN C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24134 Z= 0.225 Angle : 0.502 10.464 32800 Z= 0.252 Chirality : 0.039 0.218 3824 Planarity : 0.003 0.035 4225 Dihedral : 4.764 59.385 3409 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.16 % Favored : 98.80 % Rotamer: Outliers : 2.79 % Allowed : 15.00 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.94 (0.15), residues: 3091 helix: 2.26 (0.13), residues: 1701 sheet: -0.04 (0.24), residues: 454 loop : 0.25 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 540 HIS 0.011 0.001 HIS B 955 PHE 0.016 0.001 PHE A 352 TYR 0.010 0.001 TYR A 327 ARG 0.004 0.000 ARG B 813 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 354 time to evaluate : 2.658 Fit side-chains revert: symmetry clash REVERT: A 799 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8335 (t80) REVERT: B 135 THR cc_start: 0.7140 (p) cc_final: 0.6852 (p) REVERT: B 168 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6726 (mtp180) REVERT: B 710 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6380 (mt-10) REVERT: C 777 TYR cc_start: 0.8426 (m-80) cc_final: 0.8148 (m-80) outliers start: 70 outliers final: 57 residues processed: 399 average time/residue: 0.3559 time to fit residues: 228.3337 Evaluate side-chains 410 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 350 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 793 ASP Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 941 ILE Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.0970 chunk 293 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 283 optimal weight: 0.5980 chunk 245 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN C 120 GLN C 124 ASN C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 24134 Z= 0.166 Angle : 0.488 10.902 32800 Z= 0.243 Chirality : 0.038 0.293 3824 Planarity : 0.003 0.036 4225 Dihedral : 4.692 59.437 3409 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.07 % Favored : 98.90 % Rotamer: Outliers : 2.31 % Allowed : 15.80 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.99 (0.15), residues: 3091 helix: 2.27 (0.13), residues: 1704 sheet: 0.10 (0.25), residues: 452 loop : 0.26 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 540 HIS 0.005 0.001 HIS A 506 PHE 0.017 0.001 PHE C 511 TYR 0.010 0.001 TYR A 327 ARG 0.003 0.000 ARG B 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 356 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 799 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8311 (t80) REVERT: B 135 THR cc_start: 0.7181 (p) cc_final: 0.6842 (p) REVERT: B 168 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6695 (mtp180) REVERT: B 710 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6329 (mt-10) REVERT: B 900 MET cc_start: 0.7850 (mmp) cc_final: 0.7117 (mmt) REVERT: C 363 ARG cc_start: 0.6847 (ttm110) cc_final: 0.6566 (tpt-90) outliers start: 58 outliers final: 53 residues processed: 394 average time/residue: 0.3414 time to fit residues: 216.4098 Evaluate side-chains 405 residues out of total 2533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 349 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 942 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 710 GLU Chi-restraints excluded: chain B residue 815 GLU Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 450 SER Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 720 ASP Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 799 PHE Chi-restraints excluded: chain C residue 815 GLU Chi-restraints excluded: chain C residue 833 VAL Chi-restraints excluded: chain C residue 847 LYS Chi-restraints excluded: chain C residue 892 SER Chi-restraints excluded: chain C residue 941 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 226 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 245 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 252 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 124 ASN C 517 GLN ** C 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.092151 restraints weight = 35138.853| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.07 r_work: 0.2967 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 24134 Z= 0.183 Angle : 0.492 11.077 32800 Z= 0.245 Chirality : 0.038 0.285 3824 Planarity : 0.003 0.036 4225 Dihedral : 4.678 58.965 3409 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.13 % Favored : 98.84 % Rotamer: Outliers : 2.51 % Allowed : 15.60 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.98 (0.15), residues: 3091 helix: 2.26 (0.13), residues: 1703 sheet: 0.12 (0.25), residues: 450 loop : 0.25 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 540 HIS 0.005 0.001 HIS A 506 PHE 0.018 0.001 PHE C 511 TYR 0.010 0.001 TYR A 327 ARG 0.004 0.000 ARG C1029 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5985.83 seconds wall clock time: 108 minutes 36.50 seconds (6516.50 seconds total)