Starting phenix.real_space_refine on Fri Sep 27 23:00:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocf_12806/09_2024/7ocf_12806.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocf_12806/09_2024/7ocf_12806.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocf_12806/09_2024/7ocf_12806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocf_12806/09_2024/7ocf_12806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocf_12806/09_2024/7ocf_12806.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ocf_12806/09_2024/7ocf_12806.cif" } resolution = 3.6 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= 0.003 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 S 104 5.16 5 Cl 4 4.86 5 C 11320 2.51 5 N 2710 2.21 5 O 2950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17088 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 2803 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 23, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 220 Chain: "B" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2878 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "G" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1222 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 64 Chain: "I" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1322 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 2, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'HIS:plan': 2, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 2803 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 391} Chain breaks: 2 Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 483 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 23, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 220 Chain: "E" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1222 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 64 Chain: "J" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1322 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 2, 'TRANS': 181} Chain breaks: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'HIS:plan': 2, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2878 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 385} Chain breaks: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 131 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 147 Unusual residues: {'CYZ': 1, 'PC1': 6} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PC1:plan-2': 6} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 132 Unusual residues: {'CYZ': 1, 'PC1': 5} Classifications: {'peptide': 1, 'undetermined': 6} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PC1:plan-2': 4, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 19 Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 147 Unusual residues: {'CYZ': 1, 'PC1': 6} Classifications: {'peptide': 1, 'undetermined': 7} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PC1:plan-2': 6} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PC1:plan-2': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Unusual residues: {'CYZ': 1, 'PC1': 4} Classifications: {'peptide': 1, 'undetermined': 5} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 11.40, per 1000 atoms: 0.67 Number of scatterers: 17088 At special positions: 0 Unit cell: (116.63, 112.35, 146.59, 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) Cl 4 17.00 S 104 16.00 O 2950 8.00 N 2710 7.00 C 11320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.60 Conformation dependent library (CDL) restraints added in 2.2 seconds 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4228 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 18 sheets defined 60.2% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 419 through 433 Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.794A pdb=" N LEU A 514 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 541 Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.990A pdb=" N TRP A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 581 Processing helix chain 'A' and resid 591 through 621 removed outlier: 4.090A pdb=" N VAL A 597 " --> pdb=" O SER A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 660 through 672 removed outlier: 4.308A pdb=" N SER A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 703 through 710 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 753 through 764 Processing helix chain 'A' and resid 784 through 815 removed outlier: 4.033A pdb=" N VAL A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLY A 790 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 791 " --> pdb=" O ASN A 787 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 removed outlier: 3.557A pdb=" N LEU B 415 " --> pdb=" O HIS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.672A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.738A pdb=" N HIS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 removed outlier: 3.598A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 573 through 585 Processing helix chain 'B' and resid 595 through 618 removed outlier: 4.120A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 626 Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.641A pdb=" N GLN B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 694 Processing helix chain 'B' and resid 705 through 715 removed outlier: 3.819A pdb=" N ASN B 709 " --> pdb=" O GLU B 705 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 792 through 819 removed outlier: 4.065A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 40 removed outlier: 3.717A pdb=" N SER G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 85 removed outlier: 3.704A pdb=" N ARG G 53 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL G 69 " --> pdb=" O ARG G 65 " (cutoff:3.500A) Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 88 through 107 Proline residue: G 96 - end of helix Processing helix chain 'G' and resid 124 through 159 Processing helix chain 'I' and resid 19 through 42 removed outlier: 3.905A pdb=" N LEU I 23 " --> pdb=" O VAL I 19 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP I 42 " --> pdb=" O ALA I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 114 Processing helix chain 'I' and resid 115 through 128 Processing helix chain 'I' and resid 128 through 149 removed outlier: 3.663A pdb=" N ILE I 132 " --> pdb=" O SER I 128 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG I 149 " --> pdb=" O VAL I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 186 removed outlier: 3.638A pdb=" N LEU I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 233 removed outlier: 3.543A pdb=" N TYR I 206 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 419 through 433 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.800A pdb=" N LEU C 514 " --> pdb=" O PHE C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 541 Processing helix chain 'C' and resid 543 through 548 removed outlier: 3.993A pdb=" N TRP C 547 " --> pdb=" O SER C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 581 Processing helix chain 'C' and resid 591 through 621 removed outlier: 4.083A pdb=" N VAL C 597 " --> pdb=" O SER C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 638 Processing helix chain 'C' and resid 649 through 658 Processing helix chain 'C' and resid 660 through 672 removed outlier: 4.312A pdb=" N SER C 672 " --> pdb=" O THR C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 703 through 710 Processing helix chain 'C' and resid 739 through 752 Processing helix chain 'C' and resid 753 through 764 Processing helix chain 'C' and resid 784 through 815 removed outlier: 4.033A pdb=" N VAL C 788 " --> pdb=" O SER C 784 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY C 790 " --> pdb=" O SER C 786 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL C 791 " --> pdb=" O ASN C 787 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 40 removed outlier: 3.717A pdb=" N SER E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 85 removed outlier: 3.704A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 88 through 107 Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 124 through 159 Processing helix chain 'J' and resid 19 through 42 removed outlier: 3.904A pdb=" N LEU J 23 " --> pdb=" O VAL J 19 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP J 42 " --> pdb=" O ALA J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 114 Processing helix chain 'J' and resid 115 through 128 Processing helix chain 'J' and resid 128 through 149 removed outlier: 3.663A pdb=" N ILE J 132 " --> pdb=" O SER J 128 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG J 149 " --> pdb=" O VAL J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 186 removed outlier: 3.638A pdb=" N LEU J 159 " --> pdb=" O ARG J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 233 removed outlier: 3.542A pdb=" N TYR J 206 " --> pdb=" O GLY J 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 removed outlier: 3.557A pdb=" N LEU D 415 " --> pdb=" O HIS D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.672A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.738A pdb=" N HIS D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 removed outlier: 3.598A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 573 through 585 Processing helix chain 'D' and resid 595 through 618 removed outlier: 4.120A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA D 618 " --> pdb=" O SER D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 626 Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.642A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 694 Processing helix chain 'D' and resid 705 through 715 removed outlier: 3.819A pdb=" N ASN D 709 " --> pdb=" O GLU D 705 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU D 710 " --> pdb=" O SER D 706 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 792 through 819 removed outlier: 4.065A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 486 through 487 Processing sheet with id=AA2, first strand: chain 'A' and resid 493 through 494 Processing sheet with id=AA3, first strand: chain 'A' and resid 642 through 645 removed outlier: 6.352A pdb=" N ALA A 642 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU A 699 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLY A 644 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N GLU A 701 " --> pdb=" O GLY A 644 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N TYR A 696 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LYS A 501 " --> pdb=" O TYR A 696 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 397 through 399 removed outlier: 6.004A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA7, first strand: chain 'B' and resid 646 through 649 removed outlier: 8.478A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 80 through 82 Processing sheet with id=AA9, first strand: chain 'I' and resid 88 through 90 Processing sheet with id=AB1, first strand: chain 'C' and resid 486 through 487 Processing sheet with id=AB2, first strand: chain 'C' and resid 493 through 494 Processing sheet with id=AB3, first strand: chain 'C' and resid 642 through 645 removed outlier: 6.352A pdb=" N ALA C 642 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU C 699 " --> pdb=" O ALA C 642 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY C 644 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N GLU C 701 " --> pdb=" O GLY C 644 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N TYR C 696 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS C 501 " --> pdb=" O TYR C 696 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 80 through 82 Processing sheet with id=AB5, first strand: chain 'J' and resid 88 through 90 Processing sheet with id=AB6, first strand: chain 'D' and resid 397 through 399 removed outlier: 6.003A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AB9, first strand: chain 'D' and resid 646 through 649 removed outlier: 8.478A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) 1036 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.97 Time building geometry restraints manager: 5.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.16: 12 1.16 - 1.33: 3091 1.33 - 1.50: 7476 1.50 - 1.67: 6717 1.67 - 1.83: 166 Bond restraints: 17462 Sorted by residual: bond pdb=" C2 CYZ C1401 " pdb=" C3 CYZ C1401 " ideal model delta sigma weight residual 1.513 0.990 0.523 2.00e-02 2.50e+03 6.83e+02 bond pdb=" C2 CYZ A1401 " pdb=" C3 CYZ A1401 " ideal model delta sigma weight residual 1.513 0.991 0.522 2.00e-02 2.50e+03 6.81e+02 bond pdb=" C2 CYZ B1401 " pdb=" C3 CYZ B1401 " ideal model delta sigma weight residual 1.513 0.996 0.517 2.00e-02 2.50e+03 6.70e+02 bond pdb=" C2 CYZ D1401 " pdb=" C3 CYZ D1401 " ideal model delta sigma weight residual 1.513 0.996 0.517 2.00e-02 2.50e+03 6.69e+02 bond pdb=" C4 CYZ C1401 " pdb=" C5 CYZ C1401 " ideal model delta sigma weight residual 1.512 1.072 0.440 2.00e-02 2.50e+03 4.85e+02 ... (remaining 17457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.11: 23580 5.11 - 10.22: 108 10.22 - 15.33: 0 15.33 - 20.44: 8 20.44 - 25.55: 2 Bond angle restraints: 23698 Sorted by residual: angle pdb=" CD LYS I 102 " pdb=" CE LYS I 102 " pdb=" NZ LYS I 102 " ideal model delta sigma weight residual 111.90 86.35 25.55 3.20e+00 9.77e-02 6.38e+01 angle pdb=" CD LYS J 102 " pdb=" CE LYS J 102 " pdb=" NZ LYS J 102 " ideal model delta sigma weight residual 111.90 86.41 25.49 3.20e+00 9.77e-02 6.35e+01 angle pdb=" O3 CYZ B1401 " pdb=" S2 CYZ B1401 " pdb=" O4 CYZ B1401 " ideal model delta sigma weight residual 118.35 101.03 17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" O3 CYZ D1401 " pdb=" S2 CYZ D1401 " pdb=" O4 CYZ D1401 " ideal model delta sigma weight residual 118.35 101.08 17.27 3.00e+00 1.11e-01 3.31e+01 angle pdb=" O3 CYZ C1401 " pdb=" S2 CYZ C1401 " pdb=" O4 CYZ C1401 " ideal model delta sigma weight residual 118.35 101.12 17.23 3.00e+00 1.11e-01 3.30e+01 ... (remaining 23693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 9535 21.78 - 43.55: 511 43.55 - 65.33: 80 65.33 - 87.10: 22 87.10 - 108.88: 10 Dihedral angle restraints: 10158 sinusoidal: 3550 harmonic: 6608 Sorted by residual: dihedral pdb=" N2 CYZ B1401 " pdb=" C8 CYZ B1401 " pdb=" N1 CYZ B1401 " pdb=" S1 CYZ B1401 " ideal model delta sinusoidal sigma weight residual 55.73 -53.15 108.88 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" N2 CYZ D1401 " pdb=" C8 CYZ D1401 " pdb=" N1 CYZ D1401 " pdb=" S1 CYZ D1401 " ideal model delta sinusoidal sigma weight residual 55.73 -53.12 108.85 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C1 CYZ B1401 " pdb=" C8 CYZ B1401 " pdb=" N1 CYZ B1401 " pdb=" S1 CYZ B1401 " ideal model delta sinusoidal sigma weight residual -71.23 -175.51 104.28 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 10155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.393: 2722 0.393 - 0.785: 8 0.785 - 1.178: 0 1.178 - 1.570: 4 1.570 - 1.963: 4 Chirality restraints: 2738 Sorted by residual: chirality pdb=" C2 CYZ C1401 " pdb=" C1 CYZ C1401 " pdb=" C3 CYZ C1401 " pdb=" C7 CYZ C1401 " both_signs ideal model delta sigma weight residual False 3.31 1.35 1.96 2.00e-01 2.50e+01 9.63e+01 chirality pdb=" C2 CYZ A1401 " pdb=" C1 CYZ A1401 " pdb=" C3 CYZ A1401 " pdb=" C7 CYZ A1401 " both_signs ideal model delta sigma weight residual False 3.31 1.35 1.96 2.00e-01 2.50e+01 9.63e+01 chirality pdb=" C2 CYZ B1401 " pdb=" C1 CYZ B1401 " pdb=" C3 CYZ B1401 " pdb=" C7 CYZ B1401 " both_signs ideal model delta sigma weight residual False 3.31 1.35 1.96 2.00e-01 2.50e+01 9.57e+01 ... (remaining 2735 not shown) Planarity restraints: 2886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 403 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.30e+00 pdb=" N PRO B 404 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 403 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO D 404 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 404 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 404 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 399 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO C 400 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 400 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 400 " -0.022 5.00e-02 4.00e+02 ... (remaining 2883 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 159 2.63 - 3.20: 16621 3.20 - 3.77: 25470 3.77 - 4.33: 33810 4.33 - 4.90: 57526 Nonbonded interactions: 133586 Sorted by model distance: nonbonded pdb=" O TYR I 43 " pdb=" OG SER I 204 " model vdw 2.067 3.040 nonbonded pdb=" O TYR J 43 " pdb=" OG SER J 204 " model vdw 2.067 3.040 nonbonded pdb=" N GLU B 705 " pdb=" OE1 GLU B 705 " model vdw 2.095 3.120 nonbonded pdb=" N GLU D 705 " pdb=" OE1 GLU D 705 " model vdw 2.095 3.120 nonbonded pdb=" O GLY C 568 " pdb=" OG SER C 572 " model vdw 2.106 3.040 ... (remaining 133581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 393 through 398 and (name N or name CA or name C or name \ O or name CB )) or resid 400 through 403 or resid 405 through 407 or resid 412 t \ hrough 414 or resid 416 through 422 or resid 424 through 431 or resid 433 or res \ id 436 or resid 438 or resid 440 through 441 or resid 443 through 450 or (resid \ 452 through 454 and (name N or name CA or name C or name O or name CB )) or resi \ d 456 through 466 or (resid 468 through 469 and (name N or name CA or name C or \ name O or name CB )) or resid 471 or resid 473 through 478 or (resid 479 and (na \ me N or name CA or name C or name O or name CB )) or resid 480 through 485 or (r \ esid 486 and (name N or name CA or name C or name O or name CB )) or resid 487 t \ hrough 544 or (resid 545 through 546 and (name N or name CA or name C or name O \ or name CB )) or resid 567 through 581 or resid 583 through 628 or (resid 629 th \ rough 630 and (name N or name CA or name C or name O or name CB )) or resid 631 \ through 635 or resid 637 through 646 or resid 649 through 656 or (resid 657 and \ (name N or name CA or name C or name O or name CB )) or resid 658 through 663 or \ resid 665 through 668 or (resid 669 through 670 and (name N or name CA or name \ C or name O or name CB )) or resid 672 through 675 or (resid 676 and (name N or \ name CA or name C or name O or name CB )) or resid 677 through 682 or resid 684 \ through 685 or resid 688 through 690 or (resid 691 and (name N or name CA or nam \ e C or name O or name CB )) or resid 692 through 714 or (resid 715 and (name N o \ r name CA or name C or name O or name CB )) or resid 716 through 736 or resid 73 \ 8 or resid 741 or (resid 742 and (name N or name CA or name C or name O or name \ CB )) or resid 743 through 753 or (resid 754 and (name N or name CA or name C or \ name O or name CB )) or resid 755 through 758 or (resid 759 and (name N or name \ CA or name C or name O or name CB )) or resid 761 through 783 or (resid 784 and \ (name N or name CA or name C or name O or name CB )) or resid 785 through 795 o \ r resid 797 through 815 or resid 1401 or (resid 1402 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C \ 29 or name C2A or name C2B or name C2C or name C2D or name C2E or name O21 or na \ me O22)) or resid 1403 through 1404 or resid 1408)) selection = (chain 'B' and ((resid 397 through 402 and (name N or name CA or name C or name \ O or name CB )) or resid 404 through 405 or (resid 406 through 407 and (name N o \ r name CA or name C or name O or name CB )) or (resid 409 through 411 and (name \ N or name CA or name C or name O or name CB )) or resid 416 through 418 or (resi \ d 420 and (name N or name CA or name C or name O or name CB )) or resid 421 or ( \ resid 422 and (name N or name CA or name C or name O or name CB )) or resid 423 \ through 424 or (resid 425 through 426 and (name N or name CA or name C or name O \ or name CB )) or resid 428 through 434 or (resid 435 and (name N or name CA or \ name C or name O or name CB )) or resid 437 or resid 440 or resid 442 or resid 4 \ 44 through 445 or (resid 447 and (name N or name CA or name C or name O or name \ CB )) or resid 448 or (resid 449 and (name N or name CA or name C or name O or n \ ame CB )) or resid 450 through 452 or (resid 453 through 454 and (name N or name \ CA or name C or name O or name CB )) or resid 456 through 458 or resid 460 thro \ ugh 462 or (resid 463 and (name N or name CA or name C or name O or name CB )) o \ r resid 464 through 466 or (resid 467 and (name N or name CA or name C or name O \ or name CB )) or resid 468 through 470 or resid 472 through 473 or resid 475 or \ resid 477 through 480 or (resid 481 and (name N or name CA or name C or name O \ or name CB )) or resid 482 through 504 or (resid 505 through 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 or (resid 508 through 511 \ and (name N or name CA or name C or name O or name CB )) or resid 512 through 5 \ 85 or resid 587 through 625 or (resid 626 through 631 and (name N or name CA or \ name C or name O or name CB )) or resid 632 through 637 or (resid 638 through 63 \ 9 and (name N or name CA or name C or name O or name CB )) or (resid 641 through \ 642 and (name N or name CA or name C or name O or name CB )) or resid 643 throu \ gh 648 or (resid 649 and (name N or name CA or name C or name O or name CB )) or \ resid 650 or resid 653 through 663 or (resid 664 through 665 and (name N or nam \ e CA or name C or name O or name CB )) or resid 666 through 667 or (resid 669 th \ rough 670 and (name N or name CA or name C or name O or name CB )) or resid 671 \ or (resid 672 through 674 and (name N or name CA or name C or name O or name CB \ )) or (resid 676 through 678 and (name N or name CA or name C or name O or name \ CB )) or resid 679 through 684 or (resid 685 and (name N or name CA or name C or \ name O or name CB )) or resid 686 or resid 688 through 689 or (resid 692 and (n \ ame N or name CA or name C or name O or name CB )) or resid 693 through 704 or ( \ resid 705 and (name N or name CA or name C or name O or name CB )) or resid 706 \ through 712 or (resid 713 and (name N or name CA or name C or name O or name CB \ )) or resid 714 through 739 or (resid 740 and (name N or name CA or name C or na \ me O or name CB )) or (resid 742 and (name N or name CA or name C or name O or n \ ame CB )) or resid 745 through 751 or (resid 752 and (name N or name CA or name \ C or name O or name CB )) or resid 753 through 759 or (resid 760 through 761 and \ (name N or name CA or name C or name O or name CB )) or resid 762 through 763 o \ r (resid 765 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 66 through 774 or (resid 783 and (name N or name CA or name C or name O or name \ CB )) or resid 784 through 799 or resid 801 through 812 or (resid 813 and (name \ N or name CA or name C or name O or name CB )) or resid 814 through 816 or (resi \ d 817 through 819 and (name N or name CA or name C or name O or name CB )) or re \ sid 1401 through 1402 or (resid 1403 through 1404 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G or name O21 or name O22)) or resid 1407)) selection = (chain 'C' and ((resid 393 through 398 and (name N or name CA or name C or name \ O or name CB )) or resid 400 through 403 or resid 405 through 407 or resid 412 t \ hrough 414 or resid 416 through 422 or resid 424 through 431 or resid 433 or res \ id 436 or resid 438 or resid 440 through 441 or resid 443 through 450 or (resid \ 452 through 454 and (name N or name CA or name C or name O or name CB )) or resi \ d 456 through 466 or (resid 468 through 469 and (name N or name CA or name C or \ name O or name CB )) or resid 471 or resid 473 through 478 or (resid 479 and (na \ me N or name CA or name C or name O or name CB )) or resid 480 through 485 or (r \ esid 486 and (name N or name CA or name C or name O or name CB )) or resid 487 t \ hrough 544 or (resid 545 through 546 and (name N or name CA or name C or name O \ or name CB )) or resid 567 through 581 or resid 583 through 628 or (resid 629 th \ rough 630 and (name N or name CA or name C or name O or name CB )) or resid 631 \ through 635 or resid 637 through 646 or resid 649 through 656 or (resid 657 and \ (name N or name CA or name C or name O or name CB )) or resid 658 through 663 or \ resid 665 through 668 or (resid 669 through 670 and (name N or name CA or name \ C or name O or name CB )) or resid 672 through 675 or (resid 676 and (name N or \ name CA or name C or name O or name CB )) or resid 677 through 682 or resid 684 \ through 685 or resid 688 through 690 or (resid 691 and (name N or name CA or nam \ e C or name O or name CB )) or resid 692 through 714 or (resid 715 and (name N o \ r name CA or name C or name O or name CB )) or resid 716 through 736 or resid 73 \ 8 or resid 741 or (resid 742 and (name N or name CA or name C or name O or name \ CB )) or resid 743 through 753 or (resid 754 and (name N or name CA or name C or \ name O or name CB )) or resid 755 through 758 or (resid 759 and (name N or name \ CA or name C or name O or name CB )) or resid 761 through 783 or (resid 784 and \ (name N or name CA or name C or name O or name CB )) or resid 785 through 795 o \ r resid 797 through 815 or resid 1401 or (resid 1402 and (name C21 or name C22 o \ r name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C \ 29 or name C2A or name C2B or name C2C or name C2D or name C2E or name O21 or na \ me O22)) or resid 1403 through 1404 or resid 1408)) selection = (chain 'D' and ((resid 397 through 402 and (name N or name CA or name C or name \ O or name CB )) or resid 404 through 405 or (resid 406 through 407 and (name N o \ r name CA or name C or name O or name CB )) or (resid 409 through 411 and (name \ N or name CA or name C or name O or name CB )) or resid 416 through 418 or (resi \ d 420 and (name N or name CA or name C or name O or name CB )) or resid 421 or ( \ resid 422 and (name N or name CA or name C or name O or name CB )) or resid 423 \ through 424 or (resid 425 through 426 and (name N or name CA or name C or name O \ or name CB )) or resid 428 through 434 or (resid 435 and (name N or name CA or \ name C or name O or name CB )) or resid 437 or resid 440 or resid 442 or resid 4 \ 44 through 445 or (resid 447 and (name N or name CA or name C or name O or name \ CB )) or resid 448 or (resid 449 and (name N or name CA or name C or name O or n \ ame CB )) or resid 450 through 452 or (resid 453 through 454 and (name N or name \ CA or name C or name O or name CB )) or resid 456 through 458 or resid 460 thro \ ugh 462 or (resid 463 and (name N or name CA or name C or name O or name CB )) o \ r resid 464 through 466 or (resid 467 and (name N or name CA or name C or name O \ or name CB )) or resid 468 through 470 or resid 472 through 473 or resid 475 or \ resid 477 through 480 or (resid 481 and (name N or name CA or name C or name O \ or name CB )) or resid 482 through 504 or (resid 505 through 506 and (name N or \ name CA or name C or name O or name CB )) or resid 507 or (resid 508 through 511 \ and (name N or name CA or name C or name O or name CB )) or resid 512 through 5 \ 85 or resid 587 through 625 or (resid 626 through 631 and (name N or name CA or \ name C or name O or name CB )) or resid 632 through 637 or (resid 638 through 63 \ 9 and (name N or name CA or name C or name O or name CB )) or (resid 641 through \ 642 and (name N or name CA or name C or name O or name CB )) or resid 643 throu \ gh 648 or (resid 649 and (name N or name CA or name C or name O or name CB )) or \ resid 650 or resid 653 through 663 or (resid 664 through 665 and (name N or nam \ e CA or name C or name O or name CB )) or resid 666 through 667 or (resid 669 th \ rough 670 and (name N or name CA or name C or name O or name CB )) or resid 671 \ or (resid 672 through 674 and (name N or name CA or name C or name O or name CB \ )) or (resid 676 through 678 and (name N or name CA or name C or name O or name \ CB )) or resid 679 through 684 or (resid 685 and (name N or name CA or name C or \ name O or name CB )) or resid 686 or resid 688 through 689 or (resid 692 and (n \ ame N or name CA or name C or name O or name CB )) or resid 693 through 704 or ( \ resid 705 and (name N or name CA or name C or name O or name CB )) or resid 706 \ through 712 or (resid 713 and (name N or name CA or name C or name O or name CB \ )) or resid 714 through 739 or (resid 740 and (name N or name CA or name C or na \ me O or name CB )) or (resid 742 and (name N or name CA or name C or name O or n \ ame CB )) or resid 745 through 751 or (resid 752 and (name N or name CA or name \ C or name O or name CB )) or resid 753 through 759 or (resid 760 through 761 and \ (name N or name CA or name C or name O or name CB )) or resid 762 through 763 o \ r (resid 765 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 66 through 774 or (resid 783 and (name N or name CA or name C or name O or name \ CB )) or resid 784 through 799 or resid 801 through 812 or (resid 813 and (name \ N or name CA or name C or name O or name CB )) or resid 814 through 816 or (resi \ d 817 through 819 and (name N or name CA or name C or name O or name CB )) or re \ sid 1401 through 1402 or (resid 1403 through 1404 and (name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or name \ C2G or name O21 or name O22)) or resid 1406)) } ncs_group { reference = (chain 'E' and resid 2 through 159) selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 2.950 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: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 40.420 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 : 0.018 0.523 17462 Z= 1.220 Angle : 0.947 25.552 23698 Z= 0.395 Chirality : 0.109 1.963 2738 Planarity : 0.003 0.058 2886 Dihedral : 14.254 108.876 5906 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 0.18 (0.18), residues: 2254 helix: 1.48 (0.14), residues: 1302 sheet: -1.34 (0.39), residues: 168 loop : -1.92 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 601 HIS 0.003 0.001 HIS J 83 PHE 0.015 0.002 PHE B 574 TYR 0.013 0.001 TYR B 616 ARG 0.004 0.001 ARG C 656 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 1.618 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.8015 (mt) cc_final: 0.7806 (mt) REVERT: B 628 ARG cc_start: 0.7156 (pmt-80) cc_final: 0.6929 (pmt-80) REVERT: G 35 ARG cc_start: 0.7824 (ttp-170) cc_final: 0.7314 (ttp-170) REVERT: I 22 LEU cc_start: 0.7948 (tp) cc_final: 0.7599 (mt) REVERT: I 118 GLU cc_start: 0.7676 (tp30) cc_final: 0.7351 (tp30) REVERT: E 9 CYS cc_start: 0.8100 (m) cc_final: 0.7860 (m) REVERT: J 26 ILE cc_start: 0.8398 (mm) cc_final: 0.8125 (mt) REVERT: J 118 GLU cc_start: 0.7747 (tp30) cc_final: 0.7545 (tp30) REVERT: D 407 MET cc_start: 0.6729 (mmm) cc_final: 0.6196 (mtm) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.3138 time to fit residues: 152.5452 Evaluate side-chains 293 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 2.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 114 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 203 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN B 411 ASN C 710 GLN J 183 ASN D 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17462 Z= 0.199 Angle : 0.547 8.898 23698 Z= 0.276 Chirality : 0.040 0.159 2738 Planarity : 0.004 0.040 2886 Dihedral : 11.184 89.923 2964 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.28 % Allowed : 8.99 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: 0.96 (0.18), residues: 2254 helix: 2.06 (0.15), residues: 1326 sheet: -1.12 (0.48), residues: 96 loop : -1.59 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 460 HIS 0.004 0.001 HIS I 198 PHE 0.019 0.001 PHE D 546 TYR 0.015 0.001 TYR C 669 ARG 0.007 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 332 time to evaluate : 2.112 Fit side-chains revert: symmetry clash REVERT: A 475 LEU cc_start: 0.7807 (tt) cc_final: 0.7557 (tp) REVERT: A 485 ILE cc_start: 0.8609 (tp) cc_final: 0.8304 (tp) REVERT: A 498 ILE cc_start: 0.8004 (mt) cc_final: 0.7787 (mt) REVERT: A 711 ARG cc_start: 0.7445 (mmp80) cc_final: 0.7082 (mmp-170) REVERT: B 594 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7385 (ttp80) REVERT: G 35 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7289 (ttp-170) REVERT: I 43 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6799 (t80) REVERT: I 118 GLU cc_start: 0.7772 (tp30) cc_final: 0.7565 (tp30) REVERT: C 475 LEU cc_start: 0.7984 (tt) cc_final: 0.7771 (tp) REVERT: J 26 ILE cc_start: 0.8509 (mm) cc_final: 0.8209 (mt) outliers start: 19 outliers final: 7 residues processed: 337 average time/residue: 0.3102 time to fit residues: 152.0684 Evaluate side-chains 305 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 297 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain I residue 43 TYR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 202 optimal weight: 0.1980 chunk 69 optimal weight: 0.9990 chunk 163 optimal weight: 0.2980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 710 GLN C 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17462 Z= 0.186 Angle : 0.522 8.302 23698 Z= 0.260 Chirality : 0.040 0.195 2738 Planarity : 0.004 0.051 2886 Dihedral : 10.241 70.197 2964 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.28 % Allowed : 12.21 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2254 helix: 2.20 (0.15), residues: 1328 sheet: -1.36 (0.44), residues: 112 loop : -1.45 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 460 HIS 0.004 0.001 HIS I 105 PHE 0.015 0.001 PHE D 546 TYR 0.020 0.001 TYR D 405 ARG 0.009 0.001 ARG I 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 317 time to evaluate : 1.915 Fit side-chains revert: symmetry clash REVERT: A 485 ILE cc_start: 0.8585 (tp) cc_final: 0.8311 (tp) REVERT: A 498 ILE cc_start: 0.8033 (mt) cc_final: 0.7772 (mt) REVERT: A 629 ILE cc_start: 0.5574 (OUTLIER) cc_final: 0.5236 (mm) REVERT: A 711 ARG cc_start: 0.7397 (mmp80) cc_final: 0.7047 (mmp-170) REVERT: B 594 ARG cc_start: 0.7593 (ttp80) cc_final: 0.7331 (ttp80) REVERT: B 714 GLN cc_start: 0.8250 (mm110) cc_final: 0.7965 (mm110) REVERT: G 35 ARG cc_start: 0.7779 (ttp-170) cc_final: 0.7289 (ttp-170) REVERT: I 43 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.6771 (t80) REVERT: C 629 ILE cc_start: 0.5629 (OUTLIER) cc_final: 0.5256 (mm) REVERT: C 687 ILE cc_start: 0.7526 (mm) cc_final: 0.7276 (tp) REVERT: J 26 ILE cc_start: 0.8593 (mm) cc_final: 0.8263 (mt) REVERT: D 594 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7465 (ttp80) REVERT: D 714 GLN cc_start: 0.8174 (mm110) cc_final: 0.7893 (mm110) outliers start: 19 outliers final: 11 residues processed: 325 average time/residue: 0.3277 time to fit residues: 154.9462 Evaluate side-chains 311 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 297 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 705 ASN Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 43 TYR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 136 optimal weight: 20.0000 chunk 204 optimal weight: 0.4980 chunk 216 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 193 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17462 Z= 0.192 Angle : 0.497 8.041 23698 Z= 0.250 Chirality : 0.039 0.198 2738 Planarity : 0.003 0.038 2886 Dihedral : 9.560 58.494 2964 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.95 % Allowed : 13.69 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.18), residues: 2254 helix: 2.22 (0.15), residues: 1328 sheet: -1.13 (0.50), residues: 92 loop : -1.36 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 460 HIS 0.004 0.001 HIS J 105 PHE 0.015 0.001 PHE B 546 TYR 0.022 0.001 TYR D 405 ARG 0.008 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 318 time to evaluate : 1.923 Fit side-chains revert: symmetry clash REVERT: A 485 ILE cc_start: 0.8705 (tp) cc_final: 0.8399 (tp) REVERT: A 498 ILE cc_start: 0.8028 (mt) cc_final: 0.7800 (mt) REVERT: A 621 THR cc_start: 0.7541 (p) cc_final: 0.7294 (m) REVERT: A 629 ILE cc_start: 0.5485 (OUTLIER) cc_final: 0.5165 (mm) REVERT: A 711 ARG cc_start: 0.7352 (mmp80) cc_final: 0.7091 (mmp-170) REVERT: B 714 GLN cc_start: 0.8220 (mm110) cc_final: 0.7942 (mm-40) REVERT: G 35 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7322 (ttp-170) REVERT: I 43 TYR cc_start: 0.7365 (OUTLIER) cc_final: 0.6574 (t80) REVERT: J 26 ILE cc_start: 0.8627 (mm) cc_final: 0.8200 (mt) REVERT: D 594 ARG cc_start: 0.7648 (ttp80) cc_final: 0.7406 (ttp80) outliers start: 29 outliers final: 21 residues processed: 333 average time/residue: 0.2973 time to fit residues: 146.3347 Evaluate side-chains 328 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 305 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 43 TYR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 184 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 710 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17462 Z= 0.184 Angle : 0.494 7.950 23698 Z= 0.249 Chirality : 0.039 0.286 2738 Planarity : 0.003 0.039 2886 Dihedral : 9.213 59.218 2964 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.29 % Allowed : 12.82 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 2254 helix: 2.25 (0.15), residues: 1332 sheet: -1.00 (0.51), residues: 92 loop : -1.36 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 460 HIS 0.004 0.001 HIS I 105 PHE 0.015 0.001 PHE B 546 TYR 0.020 0.001 TYR D 405 ARG 0.005 0.000 ARG C 656 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 308 time to evaluate : 1.832 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.8021 (mt) cc_final: 0.7742 (mt) REVERT: A 629 ILE cc_start: 0.5354 (OUTLIER) cc_final: 0.5026 (mm) REVERT: A 711 ARG cc_start: 0.7433 (mmp80) cc_final: 0.7050 (mmp-170) REVERT: B 594 ARG cc_start: 0.7650 (ttp80) cc_final: 0.7375 (ttp80) REVERT: G 35 ARG cc_start: 0.7825 (ttp-170) cc_final: 0.7326 (ttp-170) REVERT: I 43 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6494 (t80) REVERT: C 629 ILE cc_start: 0.5848 (OUTLIER) cc_final: 0.5374 (mm) REVERT: C 754 VAL cc_start: 0.7531 (OUTLIER) cc_final: 0.7305 (p) REVERT: J 26 ILE cc_start: 0.8627 (mm) cc_final: 0.8180 (mt) REVERT: D 594 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7415 (ttp80) REVERT: D 714 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8102 (mt0) outliers start: 49 outliers final: 26 residues processed: 333 average time/residue: 0.3023 time to fit residues: 148.6892 Evaluate side-chains 318 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 288 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 43 TYR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 6.9990 chunk 194 optimal weight: 0.3980 chunk 42 optimal weight: 9.9990 chunk 127 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 216 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN I 183 ASN C 710 GLN ** J 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17462 Z= 0.242 Angle : 0.516 8.340 23698 Z= 0.260 Chirality : 0.040 0.266 2738 Planarity : 0.003 0.041 2886 Dihedral : 9.231 59.167 2964 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.09 % Allowed : 14.30 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.18), residues: 2254 helix: 2.11 (0.14), residues: 1346 sheet: -1.68 (0.47), residues: 122 loop : -1.33 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 460 HIS 0.003 0.001 HIS E 75 PHE 0.012 0.001 PHE E 78 TYR 0.019 0.001 TYR D 405 ARG 0.007 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 303 time to evaluate : 1.822 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.8019 (mt) cc_final: 0.7794 (mt) REVERT: A 629 ILE cc_start: 0.5293 (OUTLIER) cc_final: 0.4994 (mm) REVERT: G 35 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.7344 (ttp-170) REVERT: C 629 ILE cc_start: 0.6081 (OUTLIER) cc_final: 0.5626 (mm) REVERT: C 754 VAL cc_start: 0.7693 (OUTLIER) cc_final: 0.7455 (p) REVERT: J 26 ILE cc_start: 0.8658 (mm) cc_final: 0.8207 (mt) outliers start: 46 outliers final: 32 residues processed: 326 average time/residue: 0.3071 time to fit residues: 146.2360 Evaluate side-chains 324 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 289 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 123 optimal weight: 4.9990 chunk 158 optimal weight: 0.0870 chunk 122 optimal weight: 0.5980 chunk 182 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 chunk 131 optimal weight: 0.5980 chunk 99 optimal weight: 9.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 ASN C 710 GLN J 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17462 Z= 0.229 Angle : 0.521 8.551 23698 Z= 0.261 Chirality : 0.040 0.281 2738 Planarity : 0.003 0.040 2886 Dihedral : 9.157 59.931 2964 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.95 % Allowed : 15.57 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.18), residues: 2254 helix: 2.13 (0.14), residues: 1344 sheet: -1.98 (0.44), residues: 134 loop : -1.27 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 460 HIS 0.003 0.001 HIS I 105 PHE 0.034 0.001 PHE E 78 TYR 0.019 0.001 TYR D 405 ARG 0.012 0.001 ARG A 657 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 303 time to evaluate : 1.988 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.8006 (mt) cc_final: 0.7752 (mt) REVERT: A 629 ILE cc_start: 0.5295 (OUTLIER) cc_final: 0.5001 (mm) REVERT: B 594 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7377 (ttp80) REVERT: G 35 ARG cc_start: 0.7895 (ttp-170) cc_final: 0.7341 (ttp-170) REVERT: I 138 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8609 (mp) REVERT: C 485 ILE cc_start: 0.8549 (tp) cc_final: 0.8289 (tp) REVERT: C 629 ILE cc_start: 0.5662 (OUTLIER) cc_final: 0.5226 (mm) REVERT: C 754 VAL cc_start: 0.7816 (OUTLIER) cc_final: 0.7545 (p) REVERT: J 26 ILE cc_start: 0.8655 (mm) cc_final: 0.8204 (mt) REVERT: D 714 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8176 (mt0) outliers start: 44 outliers final: 34 residues processed: 325 average time/residue: 0.3156 time to fit residues: 150.6851 Evaluate side-chains 330 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 292 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN C 710 GLN J 183 ASN D 619 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17462 Z= 0.206 Angle : 0.512 7.938 23698 Z= 0.257 Chirality : 0.039 0.273 2738 Planarity : 0.003 0.041 2886 Dihedral : 8.946 58.808 2964 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.22 % Allowed : 16.11 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2254 helix: 2.17 (0.14), residues: 1344 sheet: -2.00 (0.42), residues: 148 loop : -1.20 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 460 HIS 0.005 0.001 HIS J 105 PHE 0.022 0.001 PHE E 78 TYR 0.017 0.001 TYR D 405 ARG 0.006 0.000 ARG C 657 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 301 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ILE cc_start: 0.8036 (mt) cc_final: 0.7769 (mt) REVERT: A 629 ILE cc_start: 0.5305 (OUTLIER) cc_final: 0.5024 (mm) REVERT: G 35 ARG cc_start: 0.7855 (ttp-170) cc_final: 0.7333 (ttp-170) REVERT: I 138 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8598 (mp) REVERT: C 485 ILE cc_start: 0.8705 (tp) cc_final: 0.8474 (tp) REVERT: C 629 ILE cc_start: 0.5602 (OUTLIER) cc_final: 0.5157 (mm) REVERT: C 726 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7899 (mtpp) REVERT: C 754 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7571 (p) REVERT: J 26 ILE cc_start: 0.8577 (mm) cc_final: 0.8131 (mt) outliers start: 48 outliers final: 34 residues processed: 324 average time/residue: 0.3158 time to fit residues: 150.3755 Evaluate side-chains 331 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 292 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 726 LYS Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 201 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 61 optimal weight: 0.0470 chunk 181 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 200 optimal weight: 0.0970 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 107 HIS I 183 ASN C 710 GLN J 183 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17462 Z= 0.201 Angle : 0.524 8.811 23698 Z= 0.262 Chirality : 0.040 0.263 2738 Planarity : 0.003 0.039 2886 Dihedral : 8.813 58.582 2964 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.95 % Allowed : 16.85 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.18), residues: 2254 helix: 2.21 (0.14), residues: 1342 sheet: -1.64 (0.38), residues: 188 loop : -1.21 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 460 HIS 0.003 0.001 HIS J 83 PHE 0.034 0.001 PHE E 78 TYR 0.016 0.001 TYR D 405 ARG 0.006 0.000 ARG A 656 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 300 time to evaluate : 1.771 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.8029 (mt) cc_final: 0.7766 (mt) REVERT: A 629 ILE cc_start: 0.5278 (OUTLIER) cc_final: 0.5005 (mm) REVERT: B 594 ARG cc_start: 0.7658 (ttp80) cc_final: 0.7424 (ttp80) REVERT: G 35 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.7372 (ttp-170) REVERT: I 138 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8596 (mp) REVERT: I 183 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7740 (t0) REVERT: C 485 ILE cc_start: 0.8756 (tp) cc_final: 0.8553 (tp) REVERT: C 629 ILE cc_start: 0.5544 (OUTLIER) cc_final: 0.5123 (mm) REVERT: C 754 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7637 (p) REVERT: J 26 ILE cc_start: 0.8574 (mm) cc_final: 0.8129 (mt) outliers start: 44 outliers final: 32 residues processed: 323 average time/residue: 0.3169 time to fit residues: 150.3958 Evaluate side-chains 332 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 295 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 153 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 785 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 223 optimal weight: 0.7980 chunk 205 optimal weight: 0.5980 chunk 177 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 ASN C 710 GLN J 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17462 Z= 0.172 Angle : 0.520 11.046 23698 Z= 0.258 Chirality : 0.040 0.262 2738 Planarity : 0.003 0.040 2886 Dihedral : 8.629 59.870 2964 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.42 % Allowed : 17.38 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.18), residues: 2254 helix: 2.27 (0.14), residues: 1342 sheet: -1.62 (0.40), residues: 174 loop : -1.10 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 460 HIS 0.005 0.001 HIS I 105 PHE 0.025 0.001 PHE E 78 TYR 0.015 0.001 TYR D 405 ARG 0.011 0.001 ARG A 657 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4508 Ramachandran restraints generated. 2254 Oldfield, 0 Emsley, 2254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 302 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 ILE cc_start: 0.8013 (mt) cc_final: 0.7751 (mt) REVERT: A 657 ARG cc_start: 0.7550 (mtm-85) cc_final: 0.7278 (mtt90) REVERT: B 594 ARG cc_start: 0.7660 (ttp80) cc_final: 0.7413 (ttp80) REVERT: I 138 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8588 (mp) REVERT: I 183 ASN cc_start: 0.7774 (OUTLIER) cc_final: 0.7523 (t0) REVERT: C 629 ILE cc_start: 0.5432 (OUTLIER) cc_final: 0.5045 (mm) REVERT: C 726 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7886 (mtpp) REVERT: C 754 VAL cc_start: 0.7884 (OUTLIER) cc_final: 0.7596 (p) REVERT: J 26 ILE cc_start: 0.8575 (mm) cc_final: 0.8134 (mt) REVERT: D 594 ARG cc_start: 0.7559 (ttp80) cc_final: 0.7314 (ttp80) outliers start: 36 outliers final: 27 residues processed: 320 average time/residue: 0.3151 time to fit residues: 147.9893 Evaluate side-chains 327 residues out of total 1938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 295 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 90 CYS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 726 LYS Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 754 VAL Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 90 CYS Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 183 ASN Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 649 THR Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.6980 chunk 189 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 163 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 49 optimal weight: 0.2980 chunk 177 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 HIS I 105 HIS C 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.171167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106535 restraints weight = 22016.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.104948 restraints weight = 15519.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105795 restraints weight = 15276.369| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.150 17462 Z= 0.236 Angle : 0.786 59.200 23698 Z= 0.464 Chirality : 0.046 0.995 2738 Planarity : 0.005 0.150 2886 Dihedral : 8.638 59.853 2964 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.35 % Allowed : 17.58 % Favored : 80.07 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.18), residues: 2254 helix: 2.25 (0.14), residues: 1342 sheet: -1.62 (0.40), residues: 174 loop : -1.10 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 460 HIS 0.006 0.001 HIS I 105 PHE 0.023 0.001 PHE E 78 TYR 0.013 0.001 TYR D 405 ARG 0.008 0.000 ARG A 657 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3628.50 seconds wall clock time: 65 minutes 28.64 seconds (3928.64 seconds total)