Starting phenix.real_space_refine on Sat Jul 4 01:16:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ocf_12806/07_2026/7ocf_12806.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ocf_12806/07_2026/7ocf_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ocf_12806/07_2026/7ocf_12806.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ocf_12806/07_2026/7ocf_12806.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ocf_12806/07_2026/7ocf_12806.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ocf_12806/07_2026/7ocf_12806.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ocf_12806/07_2026/7ocf_12806.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ocf_12806/07_2026/7ocf_12806.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'TYR:plan': 3, 'GLU:plan': 23, 'ASP:plan': 8, 'ASN:plan1': 2, 'GLN:plan1': 4, 'PHE:plan': 1, 'ARG:plan': 9, 'HIS:plan': 2} 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: {'GLU:plan': 15, 'PHE:plan': 1, 'ASP:plan': 7, 'TYR:plan': 3, 'GLN:plan1': 2, '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: {'ASP:plan': 4, 'GLU:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 3, 'ARG:plan': 3} 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: {'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 2, 'TYR:plan': 2, 'HIS:plan': 2} 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: {'TYR:plan': 3, 'GLU:plan': 23, 'ASP:plan': 8, 'ASN:plan1': 2, 'GLN:plan1': 4, 'PHE:plan': 1, 'ARG:plan': 9, 'HIS:plan': 2} 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: {'ASP:plan': 4, 'GLU:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 3, 'ARG:plan': 3} 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: {'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 2, 'TYR:plan': 2, 'HIS:plan': 2} 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: {'GLU:plan': 15, 'PHE:plan': 1, 'ASP:plan': 7, 'TYR:plan': 3, 'GLN:plan1': 2, '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: 144 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: 120 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: 46 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: 144 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: 25 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: 46 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: 95 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: 3.40, per 1000 atoms: 0.20 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: 1.57 Conformation dependent library (CDL) restraints added in 784.2 milliseconds 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: 0.38 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: 2.37 Time building geometry restraints manager: 1.94 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 - 17.80: 9197 17.80 - 35.59: 673 35.59 - 53.39: 140 53.39 - 71.19: 30 71.19 - 88.98: 14 Dihedral angle restraints: 10054 sinusoidal: 3446 harmonic: 6608 Sorted by residual: dihedral pdb=" CA ARG A 541 " pdb=" C ARG A 541 " pdb=" N PHE A 542 " pdb=" CA PHE A 542 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ARG C 541 " pdb=" C ARG C 541 " pdb=" N PHE C 542 " pdb=" CA PHE C 542 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA PHE B 571 " pdb=" C PHE B 571 " pdb=" N GLY B 572 " pdb=" CA GLY B 572 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 10051 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 1401 or (resid 1402 and (name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C2 \ A or name C2B or name C2C or name C2D or name C2E or name O21 or name O22)) or r \ esid 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 1401 or (resid 1402 and (name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C2 \ A or name C2B or name C2C or name C2D or name C2E or name O21 or name O22)) or r \ esid 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.140 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.030 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 17470 Z= 0.871 Angle : 0.947 25.552 23714 Z= 0.395 Chirality : 0.109 1.963 2738 Planarity : 0.003 0.058 2886 Dihedral : 13.476 88.984 5802 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.001 ARG C 656 TYR 0.013 0.001 TYR B 616 PHE 0.015 0.002 PHE B 574 TRP 0.009 0.001 TRP C 601 HIS 0.003 0.001 HIS J 83 Details of bonding type rmsd/Z covalent geometry : bond 0.01801 / 0.87 (17462) covalent geometry : angle 0.94684 / 0.39 (23698) SS BOND : bond 0.00179 / 0.11 ( 8) SS BOND : angle 0.63111 / 0.40 ( 16) hydrogen bonds : bond 0.12393 / 8.73 ( 1036) hydrogen bonds : angle 5.09933 / 3.61 ( 3048) *********************** 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 to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 0.388 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: 0.8397 (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: 0.1310 time to fit residues: 64.1685 Evaluate side-chains 293 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 GLN B 411 ASN C 710 GLN J 183 ASN D 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.172224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113916 restraints weight = 21999.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113719 restraints weight = 21398.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.115593 restraints weight = 16951.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115397 restraints weight = 14054.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.115661 restraints weight = 13111.601| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17470 Z= 0.147 Angle : 0.544 8.754 23714 Z= 0.278 Chirality : 0.040 0.164 2738 Planarity : 0.004 0.041 2886 Dihedral : 10.257 83.399 2860 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.28 % Allowed : 8.93 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.18), residues: 2254 helix: 2.02 (0.15), residues: 1326 sheet: -1.37 (0.43), residues: 116 loop : -1.61 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 657 TYR 0.014 0.001 TYR C 669 PHE 0.019 0.001 PHE D 546 TRP 0.023 0.001 TRP B 460 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (17462) covalent geometry : angle 0.54364 / 0.28 (23698) SS BOND : bond 0.00324 / 0.22 ( 8) SS BOND : angle 1.22068 / 0.82 ( 16) hydrogen bonds : bond 0.04147 / 2.91 ( 1036) hydrogen bonds : angle 3.94974 / 2.83 ( 3048) *********************** 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 348 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 329 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 475 LEU cc_start: 0.7867 (tt) cc_final: 0.7649 (tp) REVERT: A 485 ILE cc_start: 0.8682 (tp) cc_final: 0.8301 (tp) REVERT: A 498 ILE cc_start: 0.7953 (mt) cc_final: 0.7722 (mt) REVERT: A 711 ARG cc_start: 0.7541 (mmp80) cc_final: 0.7097 (mmp-170) REVERT: G 11 MET cc_start: 0.7732 (mtt) cc_final: 0.7464 (mtp) REVERT: G 35 ARG cc_start: 0.7696 (ttp-170) cc_final: 0.7202 (ttp-170) REVERT: I 43 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.6728 (t80) REVERT: I 102 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8545 (tmmt) REVERT: J 26 ILE cc_start: 0.8448 (mm) cc_final: 0.8116 (mt) REVERT: J 102 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8604 (tmmt) REVERT: D 487 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8260 (mt-10) outliers start: 19 outliers final: 7 residues processed: 336 average time/residue: 0.1227 time to fit residues: 60.5871 Evaluate side-chains 306 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 296 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 I residue 102 LYS 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 J residue 102 LYS 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 154 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 89 optimal weight: 0.0070 chunk 137 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 GLN C 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.172587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112838 restraints weight = 22206.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112451 restraints weight = 19942.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114636 restraints weight = 15795.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113793 restraints weight = 13104.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114228 restraints weight = 12135.357| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 0.032 17470 Z= 0.122 Angle : 0.506 8.152 23714 Z= 0.256 Chirality : 0.039 0.188 2738 Planarity : 0.004 0.053 2886 Dihedral : 9.849 82.317 2860 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.34 % Allowed : 12.21 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.18), residues: 2254 helix: 2.21 (0.15), residues: 1328 sheet: -1.35 (0.44), residues: 112 loop : -1.48 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 657 TYR 0.022 0.001 TYR D 405 PHE 0.014 0.001 PHE D 546 TRP 0.006 0.001 TRP B 460 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (17462) covalent geometry : angle 0.50584 / 0.26 (23698) SS BOND : bond 0.00365 / 0.22 ( 8) SS BOND : angle 0.87402 / 0.57 ( 16) hydrogen bonds : bond 0.03750 / 2.64 ( 1036) hydrogen bonds : angle 3.74297 / 2.69 ( 3048) *********************** 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 335 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 315 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 485 ILE cc_start: 0.8685 (tp) cc_final: 0.8304 (tp) REVERT: A 498 ILE cc_start: 0.7875 (mt) cc_final: 0.7613 (mt) REVERT: A 629 ILE cc_start: 0.5950 (OUTLIER) cc_final: 0.5620 (mm) REVERT: A 687 ILE cc_start: 0.7642 (mm) cc_final: 0.7368 (tp) REVERT: A 711 ARG cc_start: 0.7513 (mmp80) cc_final: 0.7059 (mmp-170) REVERT: B 713 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7708 (mm-30) REVERT: G 35 ARG cc_start: 0.7702 (ttp-170) cc_final: 0.7223 (ttp-170) REVERT: I 43 TYR cc_start: 0.7454 (OUTLIER) cc_final: 0.6578 (t80) REVERT: I 102 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8565 (tmmt) REVERT: C 629 ILE cc_start: 0.6035 (OUTLIER) cc_final: 0.5733 (mm) REVERT: C 687 ILE cc_start: 0.7536 (mm) cc_final: 0.7196 (tp) REVERT: J 26 ILE cc_start: 0.8465 (mm) cc_final: 0.8111 (mt) REVERT: J 102 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8595 (tmmt) REVERT: D 714 GLN cc_start: 0.8298 (mm110) cc_final: 0.8046 (mm110) outliers start: 20 outliers final: 10 residues processed: 323 average time/residue: 0.1274 time to fit residues: 60.9073 Evaluate side-chains 309 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 294 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain B residue 649 THR 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 I residue 102 LYS 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 J residue 22 LEU Chi-restraints excluded: chain J residue 43 TYR Chi-restraints excluded: chain J residue 102 LYS 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 117 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 GLN C 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.168156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.101207 restraints weight = 22161.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103681 restraints weight = 17103.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103719 restraints weight = 14386.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.103661 restraints weight = 12467.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.103873 restraints weight = 12346.965| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17470 Z= 0.176 Angle : 0.534 7.987 23714 Z= 0.271 Chirality : 0.040 0.156 2738 Planarity : 0.003 0.043 2886 Dihedral : 10.008 84.185 2860 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.55 % Allowed : 12.95 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.18), residues: 2254 helix: 2.00 (0.14), residues: 1330 sheet: -1.50 (0.47), residues: 104 loop : -1.45 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 657 TYR 0.027 0.001 TYR D 405 PHE 0.026 0.002 PHE G 78 TRP 0.009 0.001 TRP B 460 HIS 0.004 0.001 HIS J 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (17462) covalent geometry : angle 0.53399 / 0.27 (23698) SS BOND : bond 0.00198 / 0.12 ( 8) SS BOND : angle 1.01596 / 0.68 ( 16) hydrogen bonds : bond 0.04080 / 2.84 ( 1036) hydrogen bonds : angle 3.79145 / 2.72 ( 3048) *********************** 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 357 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 319 time to evaluate : 0.598 Fit side-chains REVERT: A 485 ILE cc_start: 0.8818 (tp) cc_final: 0.8357 (tp) REVERT: A 498 ILE cc_start: 0.7732 (mt) cc_final: 0.7503 (mt) REVERT: A 629 ILE cc_start: 0.6113 (OUTLIER) cc_final: 0.5804 (mm) REVERT: A 687 ILE cc_start: 0.7677 (mm) cc_final: 0.7472 (tp) REVERT: A 711 ARG cc_start: 0.7348 (mmp80) cc_final: 0.6916 (mmp-170) REVERT: B 402 GLU cc_start: 0.8293 (tp30) cc_final: 0.8084 (tp30) REVERT: B 713 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7832 (mm-30) REVERT: B 714 GLN cc_start: 0.8434 (mm110) cc_final: 0.8155 (mm-40) REVERT: G 35 ARG cc_start: 0.7488 (ttp-170) cc_final: 0.7052 (ttp-170) REVERT: I 43 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6434 (t80) REVERT: I 102 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8509 (tmmt) REVERT: C 629 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.6008 (mm) REVERT: C 711 ARG cc_start: 0.7220 (mmp80) cc_final: 0.6746 (mmp-170) REVERT: J 26 ILE cc_start: 0.8475 (mm) cc_final: 0.8022 (mt) REVERT: J 102 LYS cc_start: 0.8843 (tttm) cc_final: 0.8544 (tmmt) REVERT: D 713 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7782 (mm-30) REVERT: D 714 GLN cc_start: 0.8472 (mm110) cc_final: 0.8249 (mm-40) outliers start: 38 outliers final: 22 residues processed: 336 average time/residue: 0.1224 time to fit residues: 60.8534 Evaluate side-chains 328 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 302 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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 785 SER 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 102 LYS Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 717 MET Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 101 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 92 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 201 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 GLN B 619 ASN C 710 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.170815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3194 r_free = 0.3194 target = 0.106366 restraints weight = 22108.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.107592 restraints weight = 15724.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106931 restraints weight = 12458.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107003 restraints weight = 13456.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.107054 restraints weight = 12541.920| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17470 Z= 0.128 Angle : 0.500 8.063 23714 Z= 0.253 Chirality : 0.039 0.192 2738 Planarity : 0.003 0.042 2886 Dihedral : 9.748 82.503 2860 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.82 % Allowed : 13.49 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.18), residues: 2254 helix: 2.16 (0.15), residues: 1334 sheet: -0.68 (0.53), residues: 80 loop : -1.47 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 657 TYR 0.021 0.001 TYR D 405 PHE 0.021 0.001 PHE G 78 TRP 0.007 0.001 TRP B 460 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (17462) covalent geometry : angle 0.49930 / 0.25 (23698) SS BOND : bond 0.00218 / 0.11 ( 8) SS BOND : angle 0.75895 / 0.47 ( 16) hydrogen bonds : bond 0.03658 / 2.55 ( 1036) hydrogen bonds : angle 3.64680 / 2.63 ( 3048) *********************** 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 352 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 0.456 Fit side-chains REVERT: A 498 ILE cc_start: 0.7746 (mt) cc_final: 0.7498 (mt) REVERT: A 629 ILE cc_start: 0.5906 (OUTLIER) cc_final: 0.5619 (mm) REVERT: A 711 ARG cc_start: 0.7407 (mmp80) cc_final: 0.6773 (mmp-170) REVERT: B 402 GLU cc_start: 0.8249 (tp30) cc_final: 0.8007 (tp30) REVERT: B 422 GLU cc_start: 0.7536 (tp30) cc_final: 0.7254 (tp30) REVERT: B 713 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7806 (mm-30) REVERT: G 35 ARG cc_start: 0.7481 (ttp-170) cc_final: 0.7062 (ttp-170) REVERT: I 43 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.6286 (t80) REVERT: I 102 LYS cc_start: 0.8816 (tttm) cc_final: 0.8466 (tmmt) REVERT: C 629 ILE cc_start: 0.6284 (OUTLIER) cc_final: 0.5982 (mm) REVERT: C 711 ARG cc_start: 0.7256 (mmp80) cc_final: 0.6777 (mmp-170) REVERT: J 26 ILE cc_start: 0.8492 (mm) cc_final: 0.8036 (mt) REVERT: J 102 LYS cc_start: 0.8817 (tttm) cc_final: 0.8530 (tmmt) REVERT: D 407 MET cc_start: 0.6856 (mmm) cc_final: 0.6350 (mtt) REVERT: D 422 GLU cc_start: 0.7252 (tp30) cc_final: 0.7025 (tp30) REVERT: D 714 GLN cc_start: 0.8433 (mm110) cc_final: 0.8159 (mm-40) outliers start: 42 outliers final: 25 residues processed: 332 average time/residue: 0.1209 time to fit residues: 59.3660 Evaluate side-chains 331 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 303 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 717 MET Chi-restraints excluded: chain A residue 754 VAL 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 666 VAL Chi-restraints excluded: chain G residue 62 CYS 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 487 PHE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 62 CYS 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 464 VAL Chi-restraints excluded: chain D residue 503 MET 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 33 optimal weight: 9.9990 chunk 215 optimal weight: 0.4980 chunk 210 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 165 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 107 HIS C 710 GLN J 183 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.170445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.145447 restraints weight = 22070.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142802 restraints weight = 35563.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140512 restraints weight = 40121.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.139157 restraints weight = 44393.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137773 restraints weight = 40358.662| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 17470 Z= 0.277 Angle : 0.600 7.700 23714 Z= 0.306 Chirality : 0.043 0.214 2738 Planarity : 0.004 0.049 2886 Dihedral : 10.338 85.453 2860 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.09 % Allowed : 14.83 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 2254 helix: 1.70 (0.14), residues: 1344 sheet: -2.12 (0.44), residues: 134 loop : -1.44 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 657 TYR 0.027 0.002 TYR D 405 PHE 0.022 0.002 PHE G 78 TRP 0.009 0.001 TRP J 44 HIS 0.005 0.001 HIS I 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.28 (17462) covalent geometry : angle 0.60009 / 0.31 (23698) SS BOND : bond 0.00249 / 0.13 ( 8) SS BOND : angle 0.72121 / 0.47 ( 16) hydrogen bonds : bond 0.04565 / 3.17 ( 1036) hydrogen bonds : angle 3.92397 / 2.82 ( 3048) *********************** 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 352 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 306 time to evaluate : 0.364 Fit side-chains REVERT: A 498 ILE cc_start: 0.8016 (mt) cc_final: 0.7773 (mt) REVERT: A 629 ILE cc_start: 0.5186 (OUTLIER) cc_final: 0.4818 (mm) REVERT: G 31 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7099 (m-10) REVERT: G 35 ARG cc_start: 0.7464 (ttp-170) cc_final: 0.7042 (ttp-170) REVERT: C 629 ILE cc_start: 0.5614 (OUTLIER) cc_final: 0.5221 (mm) REVERT: C 726 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7798 (mtpp) REVERT: J 26 ILE cc_start: 0.8774 (mm) cc_final: 0.8318 (mt) outliers start: 46 outliers final: 33 residues processed: 331 average time/residue: 0.1200 time to fit residues: 58.7710 Evaluate side-chains 328 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 291 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 31 PHE Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 77 LEU 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 C residue 393 VAL 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 E residue 31 PHE Chi-restraints excluded: chain E residue 62 CYS Chi-restraints excluded: chain E residue 153 MET 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 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 736 THR 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 31 optimal weight: 0.5980 chunk 176 optimal weight: 0.7980 chunk 172 optimal weight: 0.0010 chunk 157 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 11 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 199 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 GLN B 619 ASN I 183 ASN C 710 GLN J 183 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.171384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.107148 restraints weight = 21970.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.106667 restraints weight = 15605.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106451 restraints weight = 13201.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106767 restraints weight = 12881.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.106920 restraints weight = 12574.295| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17470 Z= 0.109 Angle : 0.508 8.746 23714 Z= 0.254 Chirality : 0.039 0.207 2738 Planarity : 0.003 0.043 2886 Dihedral : 9.635 82.158 2860 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.48 % Allowed : 16.71 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.18), residues: 2254 helix: 2.11 (0.14), residues: 1344 sheet: -1.54 (0.49), residues: 104 loop : -1.39 (0.20), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 657 TYR 0.019 0.001 TYR D 405 PHE 0.021 0.001 PHE G 78 TRP 0.007 0.001 TRP B 460 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (17462) covalent geometry : angle 0.50761 / 0.25 (23698) SS BOND : bond 0.00081 / 0.05 ( 8) SS BOND : angle 0.80080 / 0.53 ( 16) hydrogen bonds : bond 0.03545 / 2.47 ( 1036) hydrogen bonds : angle 3.61744 / 2.61 ( 3048) *********************** 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 351 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 314 time to evaluate : 0.606 Fit side-chains REVERT: A 498 ILE cc_start: 0.7771 (mt) cc_final: 0.7515 (mt) REVERT: A 629 ILE cc_start: 0.5979 (OUTLIER) cc_final: 0.5720 (mm) REVERT: B 594 ARG cc_start: 0.7711 (ttp80) cc_final: 0.7454 (ttp80) REVERT: B 713 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7744 (mm-30) REVERT: G 31 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6672 (m-10) REVERT: G 35 ARG cc_start: 0.7695 (ttp-170) cc_final: 0.7217 (ttp-170) REVERT: I 138 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8369 (mp) REVERT: C 629 ILE cc_start: 0.6199 (OUTLIER) cc_final: 0.5918 (mm) REVERT: J 26 ILE cc_start: 0.8375 (mm) cc_final: 0.7921 (mt) REVERT: D 422 GLU cc_start: 0.7229 (tp30) cc_final: 0.7017 (tp30) outliers start: 37 outliers final: 24 residues processed: 331 average time/residue: 0.1219 time to fit residues: 59.6945 Evaluate side-chains 332 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 304 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 629 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 77 LEU 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 138 LEU 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 62 CYS 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 498 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 188 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 chunk 82 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 183 ASN C 710 GLN J 183 ASN D 619 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.170621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.103485 restraints weight = 22145.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.104573 restraints weight = 17936.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.105238 restraints weight = 14207.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.105519 restraints weight = 13337.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.105664 restraints weight = 12852.503| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17470 Z= 0.121 Angle : 0.515 8.036 23714 Z= 0.257 Chirality : 0.039 0.197 2738 Planarity : 0.003 0.041 2886 Dihedral : 9.288 80.496 2860 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.42 % Allowed : 17.52 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.18), residues: 2254 helix: 2.15 (0.14), residues: 1344 sheet: -1.98 (0.44), residues: 140 loop : -1.20 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 657 TYR 0.018 0.001 TYR D 405 PHE 0.014 0.001 PHE G 78 TRP 0.009 0.001 TRP B 460 HIS 0.003 0.001 HIS J 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (17462) covalent geometry : angle 0.51469 / 0.26 (23698) SS BOND : bond 0.00131 / 0.07 ( 8) SS BOND : angle 0.78187 / 0.52 ( 16) hydrogen bonds : bond 0.03550 / 2.48 ( 1036) hydrogen bonds : angle 3.58120 / 2.58 ( 3048) *********************** 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 338 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 302 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 498 ILE cc_start: 0.7780 (mt) cc_final: 0.7542 (mt) REVERT: A 683 GLU cc_start: 0.7544 (pm20) cc_final: 0.7104 (pp20) REVERT: G 31 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.6660 (m-10) REVERT: G 35 ARG cc_start: 0.7732 (ttp-170) cc_final: 0.7259 (ttp-170) REVERT: I 138 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8432 (mp) REVERT: J 26 ILE cc_start: 0.8392 (mm) cc_final: 0.7936 (mt) REVERT: D 594 ARG cc_start: 0.7807 (ttp80) cc_final: 0.7540 (ttp80) outliers start: 36 outliers final: 25 residues processed: 319 average time/residue: 0.1267 time to fit residues: 59.7980 Evaluate side-chains 320 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 293 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 B residue 464 VAL Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 77 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 138 LEU Chi-restraints excluded: chain I residue 183 ASN Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 755 LEU Chi-restraints excluded: chain E residue 62 CYS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 65 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 192 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 185 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 183 ASN C 710 GLN J 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.168719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104729 restraints weight = 22258.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.102894 restraints weight = 16255.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102924 restraints weight = 14935.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103371 restraints weight = 14348.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.103467 restraints weight = 13481.666| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17470 Z= 0.172 Angle : 0.553 8.743 23714 Z= 0.277 Chirality : 0.041 0.236 2738 Planarity : 0.003 0.044 2886 Dihedral : 9.375 82.357 2860 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.21 % Allowed : 17.79 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.18), residues: 2254 helix: 2.02 (0.14), residues: 1344 sheet: -1.94 (0.44), residues: 140 loop : -1.20 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 656 TYR 0.019 0.001 TYR D 405 PHE 0.042 0.001 PHE E 78 TRP 0.009 0.001 TRP D 766 HIS 0.005 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (17462) covalent geometry : angle 0.55262 / 0.28 (23698) SS BOND : bond 0.00134 / 0.07 ( 8) SS BOND : angle 0.79136 / 0.52 ( 16) hydrogen bonds : bond 0.03873 / 2.69 ( 1036) hydrogen bonds : angle 3.65585 / 2.63 ( 3048) *********************** 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 333 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 300 time to evaluate : 0.626 Fit side-chains REVERT: A 498 ILE cc_start: 0.7821 (mt) cc_final: 0.7590 (mt) REVERT: B 594 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7471 (ttp80) REVERT: G 31 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6788 (m-10) REVERT: G 35 ARG cc_start: 0.7737 (ttp-170) cc_final: 0.7255 (ttp-170) REVERT: C 726 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8011 (mtpp) REVERT: J 26 ILE cc_start: 0.8517 (mm) cc_final: 0.8053 (mt) outliers start: 33 outliers final: 27 residues processed: 315 average time/residue: 0.1493 time to fit residues: 69.1153 Evaluate side-chains 324 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 295 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 588 SER Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 77 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 C residue 480 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 726 LYS Chi-restraints excluded: chain C residue 755 LEU Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 62 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 51 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 147 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 GLN J 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.172992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.153249 restraints weight = 21782.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.150944 restraints weight = 37534.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.149410 restraints weight = 37069.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148706 restraints weight = 32914.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147134 restraints weight = 33658.536| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17470 Z= 0.191 Angle : 0.568 11.123 23714 Z= 0.284 Chirality : 0.041 0.255 2738 Planarity : 0.003 0.043 2886 Dihedral : 9.400 84.273 2860 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.48 % Allowed : 17.72 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.18), residues: 2254 helix: 1.95 (0.14), residues: 1344 sheet: -1.66 (0.42), residues: 156 loop : -1.22 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 657 TYR 0.019 0.001 TYR B 405 PHE 0.041 0.001 PHE E 78 TRP 0.009 0.001 TRP B 460 HIS 0.003 0.001 HIS J 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (17462) covalent geometry : angle 0.56828 / 0.28 (23698) SS BOND : bond 0.00133 / 0.07 ( 8) SS BOND : angle 0.80119 / 0.54 ( 16) hydrogen bonds : bond 0.04002 / 2.78 ( 1036) hydrogen bonds : angle 3.73693 / 2.69 ( 3048) ********************** 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 336 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 0.430 Fit side-chains REVERT: A 657 ARG cc_start: 0.6676 (mtm-85) cc_final: 0.6467 (mtt90) REVERT: G 31 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.7083 (m-10) REVERT: G 35 ARG cc_start: 0.7147 (ttp-170) cc_final: 0.6846 (ttp-170) REVERT: C 726 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7615 (mtpp) REVERT: J 26 ILE cc_start: 0.8712 (mm) cc_final: 0.8263 (mt) REVERT: J 43 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6644 (t80) outliers start: 37 outliers final: 29 residues processed: 317 average time/residue: 0.1480 time to fit residues: 69.0831 Evaluate side-chains 323 residues out of total 1938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 291 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 588 SER Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 77 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 C residue 393 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 726 LYS Chi-restraints excluded: chain C residue 755 LEU Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 62 CYS 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 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 17 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 177 optimal weight: 0.4980 chunk 95 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 209 optimal weight: 0.5980 chunk 192 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 183 ASN C 710 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.170072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105147 restraints weight = 22168.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.103958 restraints weight = 15947.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104634 restraints weight = 13270.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104598 restraints weight = 12436.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.105127 restraints weight = 11865.372| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17470 Z= 0.118 Angle : 0.530 11.963 23714 Z= 0.263 Chirality : 0.039 0.238 2738 Planarity : 0.003 0.040 2886 Dihedral : 9.009 82.436 2860 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.28 % Allowed : 18.12 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.18), residues: 2254 helix: 2.18 (0.14), residues: 1338 sheet: -1.59 (0.41), residues: 168 loop : -1.08 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 657 TYR 0.017 0.001 TYR B 405 PHE 0.034 0.001 PHE E 78 TRP 0.009 0.001 TRP B 460 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (17462) covalent geometry : angle 0.52978 / 0.26 (23698) SS BOND : bond 0.00058 / 0.04 ( 8) SS BOND : angle 0.83130 / 0.55 ( 16) hydrogen bonds : bond 0.03569 / 2.48 ( 1036) hydrogen bonds : angle 3.61031 / 2.60 ( 3048) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2712.07 seconds wall clock time: 47 minutes 39.05 seconds (2859.05 seconds total)