Starting phenix.real_space_refine on Fri Apr 12 01:02:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jg9_36225/04_2024/8jg9_36225_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jg9_36225/04_2024/8jg9_36225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jg9_36225/04_2024/8jg9_36225.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jg9_36225/04_2024/8jg9_36225.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jg9_36225/04_2024/8jg9_36225_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jg9_36225/04_2024/8jg9_36225_neut.pdb" } resolution = 3.82 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= 0.015 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: 5 Type Number sf(0) Gaussians P 220 5.49 5 S 34 5.16 5 C 14567 2.51 5 N 4203 2.21 5 O 5240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A ARG 1015": "NH1" <-> "NH2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D GLU 578": "OE1" <-> "OE2" Residue "D GLU 629": "OE1" <-> "OE2" Residue "D GLU 782": "OE1" <-> "OE2" Residue "D ARG 1015": "NH1" <-> "NH2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F GLU 151": "OE1" <-> "OE2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24264 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8436 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 25, 'TRANS': 1015} Chain breaks: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 16, 'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 111 Chain: "B" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1820 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 39, 'rna3p_pyr': 38} Link IDs: {'rna2p': 8, 'rna3p': 77} Chain breaks: 1 Chain: "D" Number of atoms: 8443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8443 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 25, 'TRANS': 1015} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 15, 'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 107 Chain: "E" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1820 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 39, 'rna3p_pyr': 38} Link IDs: {'rna2p': 8, 'rna3p': 77} Chain breaks: 1 Chain: "F" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1354 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 170} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 514 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "H" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 505 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "C" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1372 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 170} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 13.51, per 1000 atoms: 0.56 Number of scatterers: 24264 At special positions: 0 Unit cell: (130, 132.08, 176.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 220 15.00 O 5240 8.00 N 4203 7.00 C 14567 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: 10.92 Conformation dependent library (CDL) restraints added in 3.5 seconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4644 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 20 sheets defined 53.9% alpha, 9.8% beta 61 base pairs and 140 stacking pairs defined. Time for finding SS restraints: 9.38 Creating SS restraints... Processing helix chain 'A' and resid 40 through 74 removed outlier: 4.413A pdb=" N ASN A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 120 through 124 removed outlier: 4.015A pdb=" N VAL A 124 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 172 through 188 removed outlier: 3.621A pdb=" N TYR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 276 through 291 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.741A pdb=" N ILE A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.682A pdb=" N ILE A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.523A pdb=" N GLU A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 438 through 444 removed outlier: 4.188A pdb=" N ASP A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 443 " --> pdb=" O THR A 439 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 444' Processing helix chain 'A' and resid 447 through 469 Processing helix chain 'A' and resid 483 through 513 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 520 through 530 removed outlier: 3.685A pdb=" N ASP A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 549 Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 577 through 584 Processing helix chain 'A' and resid 587 through 594 Processing helix chain 'A' and resid 600 through 614 Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 619 through 627 removed outlier: 3.562A pdb=" N GLU A 624 " --> pdb=" O LYS A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 646 Processing helix chain 'A' and resid 650 through 667 Processing helix chain 'A' and resid 677 through 688 removed outlier: 3.767A pdb=" N THR A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 714 removed outlier: 3.637A pdb=" N ALA A 702 " --> pdb=" O TYR A 698 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 705 " --> pdb=" O HIS A 701 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A 712 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 713 " --> pdb=" O ALA A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 730 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 760 through 766 removed outlier: 3.900A pdb=" N LYS A 764 " --> pdb=" O ILE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 824 through 827 Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 833 through 847 removed outlier: 3.919A pdb=" N TYR A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 943 through 954 Processing helix chain 'A' and resid 1000 through 1007 Processing helix chain 'D' and resid 40 through 74 removed outlier: 4.413A pdb=" N ASN D 44 " --> pdb=" O ASN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 96 Processing helix chain 'D' and resid 101 through 115 Processing helix chain 'D' and resid 120 through 124 removed outlier: 4.015A pdb=" N VAL D 124 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 149 through 161 Processing helix chain 'D' and resid 172 through 188 removed outlier: 3.621A pdb=" N TYR D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 225 through 235 Processing helix chain 'D' and resid 250 through 265 Processing helix chain 'D' and resid 276 through 291 Processing helix chain 'D' and resid 295 through 304 Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 326 through 336 removed outlier: 3.742A pdb=" N ILE D 335 " --> pdb=" O ASP D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 removed outlier: 3.682A pdb=" N ILE D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 358 Processing helix chain 'D' and resid 360 through 371 Processing helix chain 'D' and resid 376 through 384 removed outlier: 3.523A pdb=" N GLU D 381 " --> pdb=" O GLN D 377 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 410 Processing helix chain 'D' and resid 413 through 422 Processing helix chain 'D' and resid 438 through 444 removed outlier: 4.187A pdb=" N ASP D 442 " --> pdb=" O THR D 438 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 438 through 444' Processing helix chain 'D' and resid 447 through 469 Processing helix chain 'D' and resid 483 through 513 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'D' and resid 520 through 530 removed outlier: 3.685A pdb=" N ASP D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET D 529 " --> pdb=" O LYS D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 549 removed outlier: 3.763A pdb=" N LEU D 546 " --> pdb=" O PRO D 542 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 547 " --> pdb=" O LEU D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 565 Processing helix chain 'D' and resid 568 through 570 No H-bonds generated for 'chain 'D' and resid 568 through 570' Processing helix chain 'D' and resid 577 through 584 Processing helix chain 'D' and resid 587 through 594 Processing helix chain 'D' and resid 600 through 614 Processing helix chain 'D' and resid 615 through 617 No H-bonds generated for 'chain 'D' and resid 615 through 617' Processing helix chain 'D' and resid 619 through 627 removed outlier: 3.562A pdb=" N GLU D 624 " --> pdb=" O LYS D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 646 Processing helix chain 'D' and resid 650 through 667 Processing helix chain 'D' and resid 677 through 688 removed outlier: 3.767A pdb=" N THR D 681 " --> pdb=" O ASN D 677 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 714 removed outlier: 3.637A pdb=" N ALA D 702 " --> pdb=" O TYR D 698 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA D 705 " --> pdb=" O HIS D 701 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP D 712 " --> pdb=" O ILE D 708 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE D 713 " --> pdb=" O ALA D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 720 No H-bonds generated for 'chain 'D' and resid 718 through 720' Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 746 through 755 Processing helix chain 'D' and resid 760 through 766 removed outlier: 3.900A pdb=" N LYS D 764 " --> pdb=" O ILE D 760 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 823 Processing helix chain 'D' and resid 824 through 827 Processing helix chain 'D' and resid 828 through 833 Processing helix chain 'D' and resid 833 through 847 removed outlier: 3.919A pdb=" N TYR D 837 " --> pdb=" O ASP D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 862 Processing helix chain 'D' and resid 943 through 954 Processing helix chain 'D' and resid 1000 through 1007 Processing helix chain 'F' and resid 1 through 10 Processing helix chain 'F' and resid 14 through 23 Processing helix chain 'F' and resid 25 through 35 Processing helix chain 'F' and resid 38 through 42 Processing helix chain 'F' and resid 43 through 57 removed outlier: 3.626A pdb=" N GLU F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N MET F 57 " --> pdb=" O TYR F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 Processing helix chain 'F' and resid 103 through 114 Processing helix chain 'F' and resid 116 through 121 Processing helix chain 'F' and resid 129 through 139 Processing helix chain 'F' and resid 148 through 155 Processing helix chain 'C' and resid 1 through 10 Processing helix chain 'C' and resid 14 through 23 Processing helix chain 'C' and resid 25 through 35 Processing helix chain 'C' and resid 38 through 42 Processing helix chain 'C' and resid 43 through 59 removed outlier: 3.806A pdb=" N GLU C 56 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 57 " --> pdb=" O TYR C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 96 through 100 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 116 through 121 Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 148 through 155 Processing sheet with id=AA1, first strand: chain 'A' and resid 672 through 675 removed outlier: 4.025A pdb=" N ASP A 473 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA A 31 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N SER A 772 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 33 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA3, first strand: chain 'A' and resid 553 through 557 Processing sheet with id=AA4, first strand: chain 'A' and resid 791 through 793 Processing sheet with id=AA5, first strand: chain 'A' and resid 803 through 805 Processing sheet with id=AA6, first strand: chain 'A' and resid 891 through 892 Processing sheet with id=AA7, first strand: chain 'A' and resid 922 through 929 removed outlier: 3.694A pdb=" N ALA A 964 " --> pdb=" O VAL A 916 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU A 918 " --> pdb=" O PHE A 962 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE A 962 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 933 through 936 Processing sheet with id=AA9, first strand: chain 'A' and resid 1017 through 1019 removed outlier: 7.507A pdb=" N ARG A 991 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL A 984 " --> pdb=" O ARG A 991 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU A 993 " --> pdb=" O ILE A 982 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 672 through 675 removed outlier: 4.025A pdb=" N ASP D 473 " --> pdb=" O TYR D 5 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA D 31 " --> pdb=" O LYS D 770 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N SER D 772 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL D 33 " --> pdb=" O SER D 772 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 266 through 267 Processing sheet with id=AB3, first strand: chain 'D' and resid 553 through 557 Processing sheet with id=AB4, first strand: chain 'D' and resid 791 through 793 Processing sheet with id=AB5, first strand: chain 'D' and resid 803 through 805 Processing sheet with id=AB6, first strand: chain 'D' and resid 891 through 892 Processing sheet with id=AB7, first strand: chain 'D' and resid 922 through 929 removed outlier: 3.694A pdb=" N ALA D 964 " --> pdb=" O VAL D 916 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU D 918 " --> pdb=" O PHE D 962 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE D 962 " --> pdb=" O LEU D 918 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 933 through 936 Processing sheet with id=AB9, first strand: chain 'D' and resid 1017 through 1019 removed outlier: 7.506A pdb=" N ARG D 991 " --> pdb=" O VAL D 984 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL D 984 " --> pdb=" O ARG D 991 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU D 993 " --> pdb=" O ILE D 982 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 76 through 81 Processing sheet with id=AC2, first strand: chain 'C' and resid 76 through 81 removed outlier: 3.674A pdb=" N GLU C 170 " --> pdb=" O ASP C 61 " (cutoff:3.500A) 964 hydrogen bonds defined for protein. 2775 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 270 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 140 stacking parallelities Total time for adding SS restraints: 12.62 Time building geometry restraints manager: 11.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3594 1.31 - 1.43: 7654 1.43 - 1.56: 13403 1.56 - 1.68: 436 1.68 - 1.81: 62 Bond restraints: 25149 Sorted by residual: bond pdb=" C ARG D 47 " pdb=" O ARG D 47 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.17e-02 7.31e+03 2.39e+01 bond pdb=" C ARG A 47 " pdb=" O ARG A 47 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.17e-02 7.31e+03 2.35e+01 bond pdb=" O3' U B 71 " pdb=" P U B 72 " ideal model delta sigma weight residual 1.607 1.679 -0.072 1.50e-02 4.44e+03 2.31e+01 bond pdb=" N ILE A 541 " pdb=" CA ILE A 541 " ideal model delta sigma weight residual 1.456 1.498 -0.041 8.70e-03 1.32e+04 2.27e+01 bond pdb=" O3' U E 71 " pdb=" P U E 72 " ideal model delta sigma weight residual 1.607 1.678 -0.071 1.50e-02 4.44e+03 2.27e+01 ... (remaining 25144 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.87: 1445 105.87 - 113.00: 13201 113.00 - 120.13: 11036 120.13 - 127.26: 8745 127.26 - 134.39: 528 Bond angle restraints: 34955 Sorted by residual: angle pdb=" N ARG A 51 " pdb=" CA ARG A 51 " pdb=" C ARG A 51 " ideal model delta sigma weight residual 111.28 102.87 8.41 1.09e+00 8.42e-01 5.95e+01 angle pdb=" N ARG D 51 " pdb=" CA ARG D 51 " pdb=" C ARG D 51 " ideal model delta sigma weight residual 111.28 102.91 8.37 1.09e+00 8.42e-01 5.89e+01 angle pdb=" N LEU D 110 " pdb=" CA LEU D 110 " pdb=" C LEU D 110 " ideal model delta sigma weight residual 111.28 103.45 7.83 1.09e+00 8.42e-01 5.17e+01 angle pdb=" N LEU A 110 " pdb=" CA LEU A 110 " pdb=" C LEU A 110 " ideal model delta sigma weight residual 111.28 103.45 7.83 1.09e+00 8.42e-01 5.16e+01 angle pdb=" N GLU D 45 " pdb=" CA GLU D 45 " pdb=" C GLU D 45 " ideal model delta sigma weight residual 111.82 103.56 8.26 1.16e+00 7.43e-01 5.07e+01 ... (remaining 34950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 14449 35.58 - 71.15: 875 71.15 - 106.73: 62 106.73 - 142.31: 4 142.31 - 177.88: 4 Dihedral angle restraints: 15394 sinusoidal: 8182 harmonic: 7212 Sorted by residual: dihedral pdb=" C4' U B 73 " pdb=" C3' U B 73 " pdb=" C2' U B 73 " pdb=" C1' U B 73 " ideal model delta sinusoidal sigma weight residual -35.00 33.95 -68.95 1 8.00e+00 1.56e-02 9.61e+01 dihedral pdb=" C4' U E 73 " pdb=" C3' U E 73 " pdb=" C2' U E 73 " pdb=" C1' U E 73 " ideal model delta sinusoidal sigma weight residual -35.00 33.91 -68.91 1 8.00e+00 1.56e-02 9.60e+01 dihedral pdb=" O4' U B 73 " pdb=" C2' U B 73 " pdb=" C1' U B 73 " pdb=" C3' U B 73 " ideal model delta sinusoidal sigma weight residual -35.00 31.41 -66.41 1 8.00e+00 1.56e-02 9.00e+01 ... (remaining 15391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3233 0.111 - 0.221: 678 0.221 - 0.332: 106 0.332 - 0.443: 4 0.443 - 0.553: 1 Chirality restraints: 4022 Sorted by residual: chirality pdb=" CA ASP F 61 " pdb=" N ASP F 61 " pdb=" C ASP F 61 " pdb=" CB ASP F 61 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" CA PRO D1014 " pdb=" N PRO D1014 " pdb=" C PRO D1014 " pdb=" CB PRO D1014 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA PRO A1014 " pdb=" N PRO A1014 " pdb=" C PRO A1014 " pdb=" CB PRO A1014 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 4019 not shown) Planarity restraints: 3683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 973 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C LYS D 973 " 0.063 2.00e-02 2.50e+03 pdb=" O LYS D 973 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE D 974 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 973 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C LYS A 973 " 0.063 2.00e-02 2.50e+03 pdb=" O LYS A 973 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE A 974 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1006 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLU A1006 " -0.056 2.00e-02 2.50e+03 pdb=" O GLU A1006 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A1007 " 0.019 2.00e-02 2.50e+03 ... (remaining 3680 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5728 2.79 - 3.32: 23443 3.32 - 3.85: 41547 3.85 - 4.37: 49991 4.37 - 4.90: 76178 Nonbonded interactions: 196887 Sorted by model distance: nonbonded pdb=" O ARG A 209 " pdb=" O2' U B 16 " model vdw 2.265 2.440 nonbonded pdb=" O ARG D 209 " pdb=" O2' U E 16 " model vdw 2.265 2.440 nonbonded pdb=" OG SER D 957 " pdb=" OE1 GLN D 959 " model vdw 2.271 2.440 nonbonded pdb=" OG SER A 957 " pdb=" OE1 GLN A 959 " model vdw 2.271 2.440 nonbonded pdb=" OD2 ASP D 545 " pdb=" OH TYR D 553 " model vdw 2.287 2.440 ... (remaining 196882 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' selection = (chain 'D' and (resid 1 through 542 or (resid 543 through 544 and (name N or nam \ e CA or name C or name O or name CB )) or resid 545 through 1053)) } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 0 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 20 or (resid 21 and (name N or name CA \ or name C or name O or name CB )) or resid 22 through 54 or (resid 55 through 5 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 57 through 5 \ 9 or (resid 60 and (name N or name CA or name C or name O or name CB )) or resid \ 61 through 170)) selection = (chain 'F' and (resid 0 through 51 or (resid 52 and (name N or name CA or name C \ or name O or name CB )) or resid 53 through 170)) } 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 group one per residue 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: 2.590 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: 11.090 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 76.750 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.130 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4820 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 : 0.008 0.073 25149 Z= 0.534 Angle : 1.274 10.151 34955 Z= 0.947 Chirality : 0.089 0.553 4022 Planarity : 0.005 0.041 3683 Dihedral : 19.257 177.883 10750 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.19 % Allowed : 5.62 % Favored : 93.19 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2412 helix: 0.75 (0.15), residues: 1148 sheet: -0.02 (0.36), residues: 203 loop : -0.71 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 408 HIS 0.006 0.001 HIS A 773 PHE 0.019 0.002 PHE F 165 TYR 0.027 0.002 TYR D 256 ARG 0.008 0.001 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 234 MET cc_start: -0.0683 (mmm) cc_final: -0.1233 (mtm) outliers start: 25 outliers final: 5 residues processed: 195 average time/residue: 0.4510 time to fit residues: 131.7855 Evaluate side-chains 82 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 54 GLN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 163 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 133 optimal weight: 40.0000 chunk 106 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 237 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 111 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 ASN A 411 ASN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN A 580 ASN A 695 ASN ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 ASN A 821 ASN A 863 ASN A 969 ASN A 985 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS D 75 ASN D 154 GLN D 236 HIS D 252 ASN ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN D 570 ASN D 580 ASN D 590 GLN D 695 ASN ** D 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 ASN D 930 ASN D 968 ASN F 54 GLN ** F 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5164 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 25149 Z= 0.357 Angle : 0.762 13.056 34955 Z= 0.403 Chirality : 0.044 0.231 4022 Planarity : 0.005 0.060 3683 Dihedral : 21.199 179.210 5863 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.86 % Allowed : 10.00 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2412 helix: 0.88 (0.14), residues: 1193 sheet: -0.54 (0.32), residues: 242 loop : -0.76 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 223 HIS 0.011 0.003 HIS A 330 PHE 0.021 0.002 PHE A 197 TYR 0.032 0.003 TYR A 897 ARG 0.020 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 70 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 234 MET cc_start: -0.1186 (mmm) cc_final: -0.1519 (mtp) REVERT: D 297 LYS cc_start: 0.6297 (OUTLIER) cc_final: 0.6076 (pptt) REVERT: D 1008 MET cc_start: 0.3492 (ptt) cc_final: 0.3148 (mpp) REVERT: F 57 MET cc_start: 0.5384 (mpp) cc_final: 0.5091 (ptp) outliers start: 39 outliers final: 23 residues processed: 104 average time/residue: 0.3968 time to fit residues: 66.2785 Evaluate side-chains 82 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 58 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 590 GLN Chi-restraints excluded: chain D residue 975 ASN Chi-restraints excluded: chain D residue 1032 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 163 HIS Chi-restraints excluded: chain C residue 167 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 198 optimal weight: 20.0000 chunk 162 optimal weight: 30.0000 chunk 65 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 236 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 191 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 780 ASN ** D 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS C 169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5208 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25149 Z= 0.241 Angle : 0.592 9.581 34955 Z= 0.318 Chirality : 0.039 0.228 4022 Planarity : 0.004 0.051 3683 Dihedral : 20.961 179.692 5859 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.81 % Allowed : 11.67 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2412 helix: 1.30 (0.15), residues: 1185 sheet: -0.69 (0.32), residues: 247 loop : -0.60 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 688 HIS 0.005 0.001 HIS A 111 PHE 0.024 0.002 PHE D 589 TYR 0.024 0.002 TYR D 897 ARG 0.007 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 61 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 297 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.6135 (pptt) REVERT: D 1008 MET cc_start: 0.3099 (ptt) cc_final: 0.2520 (mpp) REVERT: F 57 MET cc_start: 0.5389 (mpp) cc_final: 0.5031 (ptp) outliers start: 38 outliers final: 21 residues processed: 94 average time/residue: 0.4055 time to fit residues: 61.4455 Evaluate side-chains 74 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 52 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 975 ASN Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 167 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 5.9990 chunk 179 optimal weight: 30.0000 chunk 123 optimal weight: 0.0980 chunk 26 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 chunk 253 optimal weight: 8.9990 chunk 124 optimal weight: 0.0040 chunk 226 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 overall best weight: 2.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN D 393 HIS D 401 ASN ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 ASN D 888 ASN D 930 ASN ** F 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5212 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25149 Z= 0.181 Angle : 0.527 11.474 34955 Z= 0.285 Chirality : 0.037 0.223 4022 Planarity : 0.003 0.046 3683 Dihedral : 20.728 178.342 5854 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.00 % Allowed : 12.67 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.17), residues: 2412 helix: 1.54 (0.15), residues: 1175 sheet: -0.59 (0.32), residues: 250 loop : -0.46 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 229 HIS 0.004 0.001 HIS A 832 PHE 0.011 0.001 PHE A 664 TYR 0.017 0.001 TYR D 897 ARG 0.008 0.000 ARG F 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 52 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 MET cc_start: 0.8278 (mmt) cc_final: 0.8006 (mmp) REVERT: A 278 TYR cc_start: 0.7918 (p90) cc_final: 0.7579 (p90) REVERT: D 297 LYS cc_start: 0.6473 (pptt) cc_final: 0.6184 (pptt) REVERT: D 1008 MET cc_start: 0.2819 (ptt) cc_final: 0.2273 (mpp) REVERT: F 22 THR cc_start: 0.5728 (p) cc_final: 0.5400 (t) REVERT: F 57 MET cc_start: 0.5236 (mpp) cc_final: 0.5015 (ptp) outliers start: 42 outliers final: 20 residues processed: 92 average time/residue: 0.3667 time to fit residues: 56.1899 Evaluate side-chains 70 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 50 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1037 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 167 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 7.9990 chunk 143 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 175 optimal weight: 40.0000 chunk 0 optimal weight: 8.9990 chunk 129 optimal weight: 30.0000 chunk 227 optimal weight: 0.0040 chunk 63 optimal weight: 6.9990 overall best weight: 4.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 902 ASN ** F 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5345 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25149 Z= 0.273 Angle : 0.608 11.763 34955 Z= 0.327 Chirality : 0.039 0.241 4022 Planarity : 0.004 0.078 3683 Dihedral : 20.820 179.904 5854 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.43 % Allowed : 12.90 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2412 helix: 1.29 (0.15), residues: 1173 sheet: -0.69 (0.31), residues: 266 loop : -0.55 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 688 HIS 0.007 0.002 HIS A 890 PHE 0.018 0.002 PHE A 221 TYR 0.022 0.002 TYR D 230 ARG 0.006 0.001 ARG F 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 55 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 297 LYS cc_start: 0.6518 (OUTLIER) cc_final: 0.6285 (pptt) REVERT: D 1008 MET cc_start: 0.2764 (ptt) cc_final: 0.2508 (mpp) outliers start: 51 outliers final: 35 residues processed: 102 average time/residue: 0.3813 time to fit residues: 63.8374 Evaluate side-chains 85 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 49 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 935 LYS Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1037 ASN Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 829 MET Chi-restraints excluded: chain D residue 975 ASN Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 167 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 0.9990 chunk 228 optimal weight: 30.0000 chunk 50 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN ** A 990 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 GLN ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5425 moved from start: 0.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25149 Z= 0.303 Angle : 0.650 12.788 34955 Z= 0.344 Chirality : 0.040 0.255 4022 Planarity : 0.004 0.079 3683 Dihedral : 21.031 178.166 5854 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.81 % Allowed : 13.95 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2412 helix: 1.08 (0.15), residues: 1171 sheet: -0.61 (0.33), residues: 244 loop : -0.80 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 223 HIS 0.008 0.002 HIS A 890 PHE 0.020 0.002 PHE A 221 TYR 0.019 0.002 TYR C 53 ARG 0.006 0.001 ARG D 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 53 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.8705 (mtp) cc_final: 0.8490 (mtt) REVERT: D 297 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.5464 (pptt) REVERT: D 307 GLU cc_start: 0.6786 (pm20) cc_final: 0.6177 (mm-30) REVERT: F 147 TYR cc_start: 0.2058 (OUTLIER) cc_final: 0.1626 (p90) REVERT: F 153 PHE cc_start: 0.0908 (m-80) cc_final: 0.0676 (m-80) outliers start: 59 outliers final: 36 residues processed: 108 average time/residue: 0.3482 time to fit residues: 61.9911 Evaluate side-chains 89 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 51 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 596 ASP Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 775 VAL Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 147 TYR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 167 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 185 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 213 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 chunk 252 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 HIS ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 HIS ** A 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5542 moved from start: 0.8359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 25149 Z= 0.380 Angle : 0.752 14.261 34955 Z= 0.398 Chirality : 0.043 0.258 4022 Planarity : 0.006 0.107 3683 Dihedral : 21.363 178.046 5854 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 31.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.62 % Allowed : 14.86 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2412 helix: 0.56 (0.15), residues: 1158 sheet: -0.85 (0.33), residues: 236 loop : -1.00 (0.19), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 223 HIS 0.012 0.002 HIS A 890 PHE 0.034 0.003 PHE C 51 TYR 0.036 0.003 TYR A 771 ARG 0.007 0.001 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 53 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ASP cc_start: 0.8097 (t70) cc_final: 0.7841 (m-30) REVERT: D 232 MET cc_start: 0.6073 (mmm) cc_final: 0.5705 (mmm) REVERT: D 297 LYS cc_start: 0.6691 (OUTLIER) cc_final: 0.6374 (tmmt) REVERT: D 307 GLU cc_start: 0.6779 (pm20) cc_final: 0.6126 (mm-30) REVERT: D 844 MET cc_start: -0.2685 (ptt) cc_final: -0.2942 (ptt) REVERT: F 147 TYR cc_start: 0.2795 (OUTLIER) cc_final: 0.2413 (p90) REVERT: F 153 PHE cc_start: 0.1337 (m-80) cc_final: 0.1135 (m-80) outliers start: 55 outliers final: 41 residues processed: 104 average time/residue: 0.4146 time to fit residues: 71.3732 Evaluate side-chains 93 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 50 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 604 PHE Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 715 PHE Chi-restraints excluded: chain D residue 829 MET Chi-restraints excluded: chain D residue 997 ILE Chi-restraints excluded: chain D residue 1032 THR Chi-restraints excluded: chain F residue 51 PHE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 147 TYR Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 9.9990 chunk 100 optimal weight: 0.1980 chunk 150 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 HIS A 821 ASN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5411 moved from start: 0.8185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25149 Z= 0.179 Angle : 0.567 15.045 34955 Z= 0.300 Chirality : 0.038 0.233 4022 Planarity : 0.004 0.071 3683 Dihedral : 20.947 178.796 5854 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.71 % Allowed : 16.24 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2412 helix: 1.00 (0.15), residues: 1173 sheet: -0.85 (0.32), residues: 250 loop : -0.77 (0.20), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 408 HIS 0.006 0.001 HIS D 607 PHE 0.019 0.001 PHE C 51 TYR 0.016 0.001 TYR A 809 ARG 0.008 0.001 ARG C 2 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 52 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 784 ILE cc_start: 0.9390 (tp) cc_final: 0.9099 (mm) REVERT: A 996 MET cc_start: 0.8632 (tpp) cc_final: 0.8131 (mtp) REVERT: D 232 MET cc_start: 0.5995 (mmm) cc_final: 0.5664 (mmm) REVERT: D 297 LYS cc_start: 0.6536 (pptt) cc_final: 0.6175 (tmmt) REVERT: D 307 GLU cc_start: 0.7113 (pm20) cc_final: 0.6402 (mm-30) REVERT: D 558 ILE cc_start: 0.1838 (OUTLIER) cc_final: 0.1213 (mt) REVERT: D 844 MET cc_start: -0.2786 (ptt) cc_final: -0.3349 (ptt) REVERT: F 73 MET cc_start: 0.3286 (ptt) cc_final: 0.2950 (ptt) REVERT: F 153 PHE cc_start: 0.1112 (m-80) cc_final: 0.0863 (m-80) outliers start: 36 outliers final: 24 residues processed: 86 average time/residue: 0.3492 time to fit residues: 50.8723 Evaluate side-chains 74 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 49 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 920 ASN Chi-restraints excluded: chain D residue 926 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 142 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 8.9990 chunk 241 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 chunk 235 optimal weight: 0.5980 chunk 141 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 184 optimal weight: 30.0000 chunk 72 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 chunk 234 optimal weight: 0.7980 overall best weight: 6.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 moved from start: 0.8911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 25149 Z= 0.360 Angle : 0.705 14.370 34955 Z= 0.371 Chirality : 0.042 0.264 4022 Planarity : 0.005 0.082 3683 Dihedral : 21.143 178.495 5854 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 30.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.76 % Allowed : 16.33 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.17), residues: 2412 helix: 0.63 (0.15), residues: 1167 sheet: -1.10 (0.31), residues: 248 loop : -0.99 (0.20), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 223 HIS 0.013 0.002 HIS A 890 PHE 0.022 0.002 PHE D 690 TYR 0.025 0.002 TYR A 771 ARG 0.009 0.001 ARG A 499 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 48 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ASP cc_start: 0.8069 (t70) cc_final: 0.7830 (m-30) REVERT: D 232 MET cc_start: 0.5892 (mmm) cc_final: 0.5625 (mmm) REVERT: D 297 LYS cc_start: 0.6526 (pptt) cc_final: 0.6318 (tmmt) REVERT: D 307 GLU cc_start: 0.7145 (pm20) cc_final: 0.6275 (mm-30) REVERT: D 422 LYS cc_start: 0.5272 (tptt) cc_final: 0.4996 (tptt) REVERT: D 558 ILE cc_start: 0.1872 (OUTLIER) cc_final: 0.1237 (mt) REVERT: D 844 MET cc_start: -0.2159 (ptt) cc_final: -0.2884 (ptt) REVERT: F 73 MET cc_start: 0.3488 (ptt) cc_final: 0.3060 (ptt) outliers start: 37 outliers final: 33 residues processed: 83 average time/residue: 0.3755 time to fit residues: 51.7716 Evaluate side-chains 79 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 45 time to evaluate : 2.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 657 MET Chi-restraints excluded: chain D residue 920 ASN Chi-restraints excluded: chain D residue 926 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 40.0000 chunk 248 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 118 optimal weight: 30.0000 chunk 172 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 240 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 890 HIS ** D 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1048 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5548 moved from start: 0.9455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25149 Z= 0.316 Angle : 0.663 14.697 34955 Z= 0.350 Chirality : 0.041 0.263 4022 Planarity : 0.005 0.079 3683 Dihedral : 21.188 178.963 5854 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 27.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.62 % Allowed : 16.62 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.17), residues: 2412 helix: 0.57 (0.15), residues: 1167 sheet: -1.19 (0.34), residues: 216 loop : -1.05 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 223 HIS 0.009 0.002 HIS A 527 PHE 0.021 0.002 PHE F 153 TYR 0.025 0.002 TYR A 771 ARG 0.012 0.001 ARG A 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 48 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ASP cc_start: 0.7984 (t70) cc_final: 0.7762 (m-30) REVERT: A 996 MET cc_start: 0.8722 (tpp) cc_final: 0.8195 (mtp) REVERT: D 232 MET cc_start: 0.6039 (mmm) cc_final: 0.5773 (mmm) REVERT: D 307 GLU cc_start: 0.7150 (pm20) cc_final: 0.6369 (mm-30) REVERT: D 844 MET cc_start: -0.2338 (ptt) cc_final: -0.3113 (ptt) REVERT: F 73 MET cc_start: 0.3538 (ptt) cc_final: 0.3083 (ptt) REVERT: C 57 MET cc_start: 0.6484 (pmm) cc_final: 0.6109 (pmm) outliers start: 34 outliers final: 30 residues processed: 82 average time/residue: 0.3767 time to fit residues: 51.4291 Evaluate side-chains 74 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 44 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 1000 THR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 327 LYS Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 920 ASN Chi-restraints excluded: chain D residue 926 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 9.9990 chunk 221 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 191 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 888 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1048 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.067408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.054580 restraints weight = 249166.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.053247 restraints weight = 235123.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.052922 restraints weight = 216956.034| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 1.0289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 25149 Z= 0.390 Angle : 0.758 14.371 34955 Z= 0.398 Chirality : 0.044 0.282 4022 Planarity : 0.005 0.093 3683 Dihedral : 21.451 179.478 5854 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 34.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.00 % Allowed : 16.33 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 2412 helix: 0.27 (0.15), residues: 1156 sheet: -1.48 (0.34), residues: 210 loop : -1.21 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 223 HIS 0.011 0.002 HIS A 890 PHE 0.020 0.003 PHE A 221 TYR 0.029 0.003 TYR A 771 ARG 0.013 0.001 ARG A 499 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3476.18 seconds wall clock time: 71 minutes 54.90 seconds (4314.90 seconds total)