Starting phenix.real_space_refine on Thu Feb 15 18:41:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3e_23652/02_2024/7m3e_23652_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3e_23652/02_2024/7m3e_23652.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3e_23652/02_2024/7m3e_23652_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3e_23652/02_2024/7m3e_23652_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3e_23652/02_2024/7m3e_23652_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3e_23652/02_2024/7m3e_23652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3e_23652/02_2024/7m3e_23652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3e_23652/02_2024/7m3e_23652_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m3e_23652/02_2024/7m3e_23652_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.027 sd= 0.628 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 2 5.49 5 S 74 5.16 5 Cl 2 4.86 5 C 8477 2.51 5 N 2111 2.21 5 O 2421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 248": "OD1" <-> "OD2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A ASP 410": "OD1" <-> "OD2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 671": "OE1" <-> "OE2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 873": "NH1" <-> "NH2" Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B GLU 475": "OE1" <-> "OE2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B GLU 519": "OE1" <-> "OE2" Residue "B PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 602": "OE1" <-> "OE2" Residue "B PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 649": "OE1" <-> "OE2" Residue "B PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 873": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13091 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6410 Classifications: {'peptide': 810} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 31, 'TRANS': 778} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 6425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 812, 6425 Classifications: {'peptide': 812} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 31, 'TRANS': 780} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 108 Unusual residues: {' CA': 3, 'NAG': 4, 'PO4': 1, 'YP1': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A 906 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 120 Unusual residues: {' CA': 1, 'NAG': 5, 'PO4': 1, 'YP1': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B 907 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.89, per 1000 atoms: 0.53 Number of scatterers: 13091 At special positions: 0 Unit cell: (103.194, 99.0108, 192.443, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 4 19.99 Cl 2 17.00 S 74 16.00 P 2 15.00 O 2421 8.00 N 2111 7.00 C 8477 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.04 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.02 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=2.04 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.04 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 902 " - " ASN A 261 " " NAG A 903 " - " ASN A 287 " " NAG A 904 " - " ASN A 488 " " NAG A 905 " - " ASN A 468 " " NAG B 902 " - " ASN B 541 " " NAG B 903 " - " ASN B 261 " " NAG B 904 " - " ASN B 287 " " NAG B 905 " - " ASN B 488 " " NAG B 906 " - " ASN B 468 " " NAG C 1 " - " ASN A 541 " Time building additional restraints: 4.98 Conformation dependent library (CDL) restraints added in 2.3 seconds 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 13 sheets defined 40.8% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 65 through 83 Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.685A pdb=" N ALA A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.610A pdb=" N ILE A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 157 removed outlier: 3.638A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 191 through 204 Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.862A pdb=" N GLU A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 261 removed outlier: 3.570A pdb=" N ASN A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 308 through 314 removed outlier: 4.912A pdb=" N HIS A 312 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 314 " --> pdb=" O PHE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.858A pdb=" N LYS A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 removed outlier: 3.538A pdb=" N PHE A 356 " --> pdb=" O TRP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.611A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 611 through 636 removed outlier: 3.907A pdb=" N GLY A 623 " --> pdb=" O PHE A 619 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 648 through 652 Processing helix chain 'A' and resid 654 through 665 removed outlier: 3.749A pdb=" N LEU A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 678 Processing helix chain 'A' and resid 680 through 696 removed outlier: 3.989A pdb=" N PHE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 745 removed outlier: 3.981A pdb=" N LEU A 730 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 731 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A 738 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 743 " --> pdb=" O CYS A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 794 removed outlier: 3.853A pdb=" N LEU A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 777 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 793 " --> pdb=" O PHE A 789 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER A 794 " --> pdb=" O PHE A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 827 removed outlier: 3.635A pdb=" N PHE A 815 " --> pdb=" O MET A 811 " (cutoff:3.500A) Proline residue: A 823 - end of helix removed outlier: 4.056A pdb=" N ALA A 826 " --> pdb=" O ILE A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 850 removed outlier: 3.812A pdb=" N ILE A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 861 Processing helix chain 'A' and resid 863 through 865 No H-bonds generated for 'chain 'A' and resid 863 through 865' Processing helix chain 'B' and resid 65 through 82 removed outlier: 3.739A pdb=" N MET B 74 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 114 removed outlier: 3.674A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 123 removed outlier: 3.598A pdb=" N ILE B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP B 121 " --> pdb=" O GLN B 117 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 159 removed outlier: 3.784A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 273 through 286 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 308 through 314 removed outlier: 4.754A pdb=" N HIS B 312 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL B 314 " --> pdb=" O PHE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 348 through 356 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 417 through 435 removed outlier: 4.123A pdb=" N ILE B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 525 through 527 No H-bonds generated for 'chain 'B' and resid 525 through 527' Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 593 through 595 No H-bonds generated for 'chain 'B' and resid 593 through 595' Processing helix chain 'B' and resid 611 through 636 removed outlier: 3.650A pdb=" N LEU B 618 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE B 619 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 620 " --> pdb=" O LEU B 616 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 623 " --> pdb=" O PHE B 619 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 624 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE B 629 " --> pdb=" O PHE B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 645 Processing helix chain 'B' and resid 648 through 665 removed outlier: 3.526A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 678 No H-bonds generated for 'chain 'B' and resid 675 through 678' Processing helix chain 'B' and resid 680 through 696 removed outlier: 3.970A pdb=" N PHE B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 745 removed outlier: 3.902A pdb=" N LEU B 730 " --> pdb=" O LEU B 726 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N CYS B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE B 738 " --> pdb=" O MET B 734 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 743 " --> pdb=" O CYS B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 794 removed outlier: 3.582A pdb=" N LEU B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR B 780 " --> pdb=" O LEU B 776 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER B 794 " --> pdb=" O PHE B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 826 removed outlier: 3.623A pdb=" N PHE B 815 " --> pdb=" O MET B 811 " (cutoff:3.500A) Proline residue: B 823 - end of helix removed outlier: 4.383A pdb=" N ALA B 826 " --> pdb=" O ILE B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 861 removed outlier: 3.759A pdb=" N ILE B 841 " --> pdb=" O GLU B 837 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 844 " --> pdb=" O ALA B 840 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE B 846 " --> pdb=" O LEU B 842 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N CYS B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ILE B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE B 853 " --> pdb=" O LEU B 849 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 865 No H-bonds generated for 'chain 'B' and resid 863 through 865' Processing sheet with id= A, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.196A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLY A 35 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL A 141 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU A 37 " --> pdb=" O VAL A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 240 through 243 removed outlier: 9.526A pdb=" N GLU A 241 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR A 211 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ILE A 243 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 213 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL A 266 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE A 212 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL A 268 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ALA A 214 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N PHE A 270 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE A 292 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL A 269 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU A 294 " --> pdb=" O VAL A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 318 through 321 removed outlier: 6.534A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 468 through 470 Processing sheet with id= E, first strand: chain 'A' and resid 550 through 552 Processing sheet with id= F, first strand: chain 'A' and resid 589 through 591 Processing sheet with id= G, first strand: chain 'A' and resid 602 through 604 removed outlier: 3.720A pdb=" N ILE A 763 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.386A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B 139 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY B 35 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 141 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU B 37 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 240 through 243 removed outlier: 9.544A pdb=" N GLU B 241 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR B 211 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE B 243 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA B 213 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 266 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE B 212 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL B 268 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ALA B 214 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE B 270 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE B 292 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL B 269 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU B 294 " --> pdb=" O VAL B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 318 through 321 removed outlier: 6.402A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N PHE B 505 " --> pdb=" O HIS B 495 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 468 through 470 Processing sheet with id= L, first strand: chain 'B' and resid 589 through 591 Processing sheet with id= M, first strand: chain 'B' and resid 602 through 604 removed outlier: 3.669A pdb=" N ILE B 763 " --> pdb=" O GLU B 604 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 5.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2109 1.29 - 1.43: 3683 1.43 - 1.56: 7525 1.56 - 1.69: 4 1.69 - 1.83: 90 Bond restraints: 13411 Sorted by residual: bond pdb=" C15 YP1 A 901 " pdb=" N2 YP1 A 901 " ideal model delta sigma weight residual 1.457 1.549 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C15 YP1 B 901 " pdb=" N2 YP1 B 901 " ideal model delta sigma weight residual 1.457 1.549 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C2 YP1 A 901 " pdb=" N2 YP1 A 901 " ideal model delta sigma weight residual 1.458 1.544 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C2 YP1 B 901 " pdb=" N2 YP1 B 901 " ideal model delta sigma weight residual 1.458 1.544 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" O4 PO4 B 909 " pdb=" P PO4 B 909 " ideal model delta sigma weight residual 1.568 1.495 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 13406 not shown) Histogram of bond angle deviations from ideal: 99.70 - 115.64: 8440 115.64 - 131.58: 9722 131.58 - 147.52: 35 147.52 - 163.45: 0 163.45 - 179.39: 2 Bond angle restraints: 18199 Sorted by residual: angle pdb=" C TYR A 411 " pdb=" N THR A 412 " pdb=" CA THR A 412 " ideal model delta sigma weight residual 121.54 133.13 -11.59 1.91e+00 2.74e-01 3.68e+01 angle pdb=" CA PRO B 823 " pdb=" N PRO B 823 " pdb=" CD PRO B 823 " ideal model delta sigma weight residual 112.00 104.66 7.34 1.40e+00 5.10e-01 2.75e+01 angle pdb=" CA PRO A 823 " pdb=" N PRO A 823 " pdb=" CD PRO A 823 " ideal model delta sigma weight residual 112.00 104.77 7.23 1.40e+00 5.10e-01 2.67e+01 angle pdb=" C ARG B 638 " pdb=" N ASN B 639 " pdb=" CA ASN B 639 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C ARG A 638 " pdb=" N ASN A 639 " pdb=" CA ASN A 639 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.48e+01 ... (remaining 18194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 7701 25.74 - 51.48: 281 51.48 - 77.22: 29 77.22 - 102.96: 11 102.96 - 128.69: 4 Dihedral angle restraints: 8026 sinusoidal: 3302 harmonic: 4724 Sorted by residual: dihedral pdb=" CA ARG A 54 " pdb=" C ARG A 54 " pdb=" N PRO A 55 " pdb=" CA PRO A 55 " ideal model delta harmonic sigma weight residual 180.00 -153.13 -26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA GLN A 260 " pdb=" C GLN A 260 " pdb=" N ASN A 261 " pdb=" CA ASN A 261 " ideal model delta harmonic sigma weight residual 180.00 153.56 26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA SER A 53 " pdb=" C SER A 53 " pdb=" N ARG A 54 " pdb=" CA ARG A 54 " ideal model delta harmonic sigma weight residual -180.00 -154.00 -26.00 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 8023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1974 0.127 - 0.254: 72 0.254 - 0.381: 0 0.381 - 0.508: 3 0.508 - 0.635: 3 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CB ILE A 822 " pdb=" CA ILE A 822 " pdb=" CG1 ILE A 822 " pdb=" CG2 ILE A 822 " both_signs ideal model delta sigma weight residual False 2.64 2.01 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CB ILE B 822 " pdb=" CA ILE B 822 " pdb=" CG1 ILE B 822 " pdb=" CG2 ILE B 822 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.58 2.00e-01 2.50e+01 8.33e+00 chirality pdb=" CB ILE A 869 " pdb=" CA ILE A 869 " pdb=" CG1 ILE A 869 " pdb=" CG2 ILE A 869 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.74e+00 ... (remaining 2049 not shown) Planarity restraints: 2301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 YP1 B 901 " -0.050 2.00e-02 2.50e+03 1.00e-01 2.52e+02 pdb=" C19 YP1 B 901 " -0.007 2.00e-02 2.50e+03 pdb=" C20 YP1 B 901 " -0.021 2.00e-02 2.50e+03 pdb=" C21 YP1 B 901 " 0.066 2.00e-02 2.50e+03 pdb=" C22 YP1 B 901 " 0.108 2.00e-02 2.50e+03 pdb=" C23 YP1 B 901 " 0.028 2.00e-02 2.50e+03 pdb=" C24 YP1 B 901 " 0.070 2.00e-02 2.50e+03 pdb=" N1 YP1 B 901 " 0.141 2.00e-02 2.50e+03 pdb=" O1 YP1 B 901 " -0.163 2.00e-02 2.50e+03 pdb="CL1 YP1 B 901 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 YP1 A 901 " 0.049 2.00e-02 2.50e+03 1.00e-01 2.51e+02 pdb=" C19 YP1 A 901 " 0.007 2.00e-02 2.50e+03 pdb=" C20 YP1 A 901 " 0.021 2.00e-02 2.50e+03 pdb=" C21 YP1 A 901 " -0.066 2.00e-02 2.50e+03 pdb=" C22 YP1 A 901 " -0.108 2.00e-02 2.50e+03 pdb=" C23 YP1 A 901 " -0.028 2.00e-02 2.50e+03 pdb=" C24 YP1 A 901 " -0.069 2.00e-02 2.50e+03 pdb=" N1 YP1 A 901 " -0.142 2.00e-02 2.50e+03 pdb=" O1 YP1 A 901 " 0.163 2.00e-02 2.50e+03 pdb="CL1 YP1 A 901 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 822 " -0.090 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO A 823 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO A 823 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 823 " -0.072 5.00e-02 4.00e+02 ... (remaining 2298 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3013 2.79 - 3.32: 11015 3.32 - 3.85: 20001 3.85 - 4.37: 23860 4.37 - 4.90: 42520 Nonbonded interactions: 100409 Sorted by model distance: nonbonded pdb=" O PHE B 351 " pdb=" OG1 THR B 355 " model vdw 2.265 2.440 nonbonded pdb=" OD2 ASP B 238 " pdb=" OG SER B 262 " model vdw 2.296 2.440 nonbonded pdb=" OH TYR B 203 " pdb=" OE2 GLU B 525 " model vdw 2.302 2.440 nonbonded pdb=" NH1 ARG A 69 " pdb=" O PRO A 407 " model vdw 2.309 2.520 nonbonded pdb=" NH1 ARG B 69 " pdb=" O PRO B 407 " model vdw 2.316 2.520 ... (remaining 100404 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 876 or resid 901 through 905 or resid 909 throu \ gh 910)) selection = (chain 'B' and (resid 20 through 361 or resid 391 through 553 or (resid 554 and \ (name N or name CA or name C or name O or name CB )) or resid 555 through 706 or \ (resid 721 and (name N or name CA or name C or name O or name CB )) or resid 72 \ 2 through 876 or resid 901 through 905 or resid 908 through 909)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.990 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 36.510 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.006 0.092 13411 Z= 0.404 Angle : 0.946 11.593 18199 Z= 0.518 Chirality : 0.062 0.635 2052 Planarity : 0.009 0.132 2291 Dihedral : 13.623 128.694 4917 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.18), residues: 1606 helix: -1.87 (0.16), residues: 690 sheet: -1.29 (0.36), residues: 212 loop : -1.76 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 299 HIS 0.005 0.001 HIS A 463 PHE 0.043 0.003 PHE B 788 TYR 0.057 0.003 TYR A 573 ARG 0.015 0.001 ARG B 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.492 Fit side-chains REVERT: A 729 PHE cc_start: 0.8120 (t80) cc_final: 0.7911 (t80) REVERT: B 205 ARG cc_start: 0.7183 (mtp180) cc_final: 0.6524 (mtp180) REVERT: B 575 ASP cc_start: 0.7395 (p0) cc_final: 0.6956 (p0) REVERT: B 577 THR cc_start: 0.8757 (m) cc_final: 0.8536 (m) REVERT: B 729 PHE cc_start: 0.7855 (t80) cc_final: 0.7651 (t80) REVERT: B 858 TYR cc_start: 0.8237 (t80) cc_final: 0.7949 (t80) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2704 time to fit residues: 71.3430 Evaluate side-chains 164 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 147 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 ASN B 673 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13411 Z= 0.219 Angle : 0.572 9.708 18199 Z= 0.300 Chirality : 0.045 0.292 2052 Planarity : 0.005 0.082 2291 Dihedral : 8.509 118.697 1977 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.72 % Allowed : 5.36 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.19), residues: 1606 helix: -0.72 (0.19), residues: 692 sheet: -1.13 (0.36), residues: 208 loop : -1.67 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 299 HIS 0.005 0.001 HIS B 359 PHE 0.023 0.001 PHE B 330 TYR 0.015 0.002 TYR A 435 ARG 0.005 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 1.577 Fit side-chains REVERT: B 205 ARG cc_start: 0.7338 (mtp180) cc_final: 0.6712 (mtp180) REVERT: B 858 TYR cc_start: 0.8359 (t80) cc_final: 0.8059 (t80) outliers start: 10 outliers final: 7 residues processed: 174 average time/residue: 0.2522 time to fit residues: 63.8745 Evaluate side-chains 174 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 644 LYS Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 147 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN A 800 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 13411 Z= 0.438 Angle : 0.692 10.399 18199 Z= 0.357 Chirality : 0.050 0.289 2052 Planarity : 0.005 0.071 2291 Dihedral : 8.451 119.679 1977 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.22 % Allowed : 7.65 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.20), residues: 1606 helix: -0.50 (0.19), residues: 697 sheet: -1.18 (0.38), residues: 189 loop : -1.83 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 299 HIS 0.006 0.001 HIS B 495 PHE 0.032 0.002 PHE B 330 TYR 0.029 0.003 TYR A 411 ARG 0.011 0.001 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 1.856 Fit side-chains REVERT: A 578 ASP cc_start: 0.7660 (t0) cc_final: 0.7272 (t70) REVERT: B 205 ARG cc_start: 0.7340 (mtp180) cc_final: 0.7084 (mmm160) REVERT: B 575 ASP cc_start: 0.7635 (p0) cc_final: 0.7264 (p0) REVERT: B 635 ILE cc_start: 0.9038 (mt) cc_final: 0.8671 (mt) outliers start: 17 outliers final: 15 residues processed: 175 average time/residue: 0.2634 time to fit residues: 67.0188 Evaluate side-chains 180 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 165 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 644 LYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 644 LYS Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 76 optimal weight: 0.0470 chunk 16 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 ASN B 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13411 Z= 0.228 Angle : 0.563 9.701 18199 Z= 0.293 Chirality : 0.045 0.271 2052 Planarity : 0.004 0.063 2291 Dihedral : 7.835 113.907 1977 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.22 % Allowed : 9.30 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.20), residues: 1606 helix: -0.07 (0.20), residues: 696 sheet: -1.20 (0.37), residues: 206 loop : -1.73 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 299 HIS 0.004 0.001 HIS B 359 PHE 0.015 0.001 PHE B 330 TYR 0.013 0.002 TYR A 435 ARG 0.004 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 164 time to evaluate : 1.533 Fit side-chains REVERT: A 270 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8001 (t80) REVERT: A 578 ASP cc_start: 0.7640 (t0) cc_final: 0.7285 (t70) REVERT: B 205 ARG cc_start: 0.7294 (mtp180) cc_final: 0.7046 (mmm160) REVERT: B 635 ILE cc_start: 0.8984 (mt) cc_final: 0.8606 (mt) REVERT: B 641 PRO cc_start: 0.8163 (Cg_exo) cc_final: 0.7751 (Cg_endo) outliers start: 17 outliers final: 12 residues processed: 173 average time/residue: 0.2613 time to fit residues: 66.0534 Evaluate side-chains 173 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 644 LYS Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 0.0970 chunk 133 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13411 Z= 0.293 Angle : 0.595 9.913 18199 Z= 0.307 Chirality : 0.047 0.278 2052 Planarity : 0.004 0.054 2291 Dihedral : 7.793 112.659 1977 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.93 % Allowed : 9.08 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.20), residues: 1606 helix: 0.03 (0.20), residues: 701 sheet: -1.19 (0.38), residues: 206 loop : -1.80 (0.21), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 299 HIS 0.004 0.001 HIS B 359 PHE 0.017 0.002 PHE B 330 TYR 0.019 0.002 TYR A 573 ARG 0.006 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.360 Fit side-chains REVERT: A 270 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.7998 (t80) REVERT: A 573 TYR cc_start: 0.6940 (p90) cc_final: 0.6590 (p90) REVERT: A 578 ASP cc_start: 0.7659 (t0) cc_final: 0.7280 (t70) REVERT: B 205 ARG cc_start: 0.7394 (mtp180) cc_final: 0.7107 (mmm160) REVERT: B 635 ILE cc_start: 0.8995 (mt) cc_final: 0.8631 (mt) REVERT: B 641 PRO cc_start: 0.8145 (Cg_exo) cc_final: 0.7743 (Cg_endo) REVERT: B 649 GLU cc_start: 0.7627 (mp0) cc_final: 0.7357 (mp0) outliers start: 27 outliers final: 23 residues processed: 173 average time/residue: 0.2640 time to fit residues: 66.1418 Evaluate side-chains 183 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 644 LYS Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 644 LYS Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.0070 chunk 51 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13411 Z= 0.219 Angle : 0.545 9.708 18199 Z= 0.283 Chirality : 0.045 0.271 2052 Planarity : 0.004 0.050 2291 Dihedral : 7.544 111.349 1977 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.93 % Allowed : 10.23 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.20), residues: 1606 helix: 0.27 (0.20), residues: 694 sheet: -1.15 (0.38), residues: 206 loop : -1.69 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 299 HIS 0.004 0.001 HIS B 359 PHE 0.012 0.001 PHE B 311 TYR 0.014 0.002 TYR A 573 ARG 0.004 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 time to evaluate : 1.487 Fit side-chains REVERT: A 270 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8020 (t80) REVERT: A 573 TYR cc_start: 0.6766 (p90) cc_final: 0.6410 (p90) REVERT: B 205 ARG cc_start: 0.7371 (mtp180) cc_final: 0.7076 (mmm160) REVERT: B 635 ILE cc_start: 0.8986 (mt) cc_final: 0.8617 (mt) REVERT: B 641 PRO cc_start: 0.8118 (Cg_exo) cc_final: 0.7732 (Cg_endo) outliers start: 27 outliers final: 21 residues processed: 177 average time/residue: 0.2724 time to fit residues: 69.8974 Evaluate side-chains 183 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 644 LYS Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 114 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13411 Z= 0.204 Angle : 0.537 9.756 18199 Z= 0.278 Chirality : 0.045 0.273 2052 Planarity : 0.004 0.046 2291 Dihedral : 7.416 111.074 1977 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.15 % Allowed : 10.30 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.20), residues: 1606 helix: 0.42 (0.20), residues: 695 sheet: -1.11 (0.38), residues: 206 loop : -1.67 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 299 HIS 0.004 0.001 HIS B 359 PHE 0.011 0.001 PHE B 311 TYR 0.012 0.001 TYR A 573 ARG 0.004 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 1.652 Fit side-chains REVERT: A 270 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8015 (t80) REVERT: A 573 TYR cc_start: 0.6619 (p90) cc_final: 0.6332 (p90) REVERT: B 205 ARG cc_start: 0.7281 (mtp180) cc_final: 0.7043 (mmm160) REVERT: B 394 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7647 (mp) REVERT: B 635 ILE cc_start: 0.8977 (mt) cc_final: 0.8607 (mt) REVERT: B 641 PRO cc_start: 0.8088 (Cg_exo) cc_final: 0.7715 (Cg_endo) outliers start: 30 outliers final: 26 residues processed: 179 average time/residue: 0.2503 time to fit residues: 65.4393 Evaluate side-chains 185 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 749 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 644 LYS Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 828 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 47 optimal weight: 0.0000 chunk 30 optimal weight: 0.0060 chunk 99 optimal weight: 0.5980 chunk 106 optimal weight: 0.0470 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 0.0040 chunk 122 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 overall best weight: 0.1310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13411 Z= 0.116 Angle : 0.474 9.500 18199 Z= 0.247 Chirality : 0.042 0.241 2052 Planarity : 0.004 0.058 2291 Dihedral : 6.966 109.555 1977 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.36 % Allowed : 11.09 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1606 helix: 0.83 (0.20), residues: 695 sheet: -1.19 (0.37), residues: 202 loop : -1.38 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 208 HIS 0.004 0.001 HIS B 359 PHE 0.012 0.001 PHE B 539 TYR 0.008 0.001 TYR A 573 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 1.473 Fit side-chains REVERT: A 270 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.7953 (t80) REVERT: B 635 ILE cc_start: 0.8935 (mt) cc_final: 0.8550 (mt) REVERT: B 641 PRO cc_start: 0.8030 (Cg_exo) cc_final: 0.7719 (Cg_endo) REVERT: B 729 PHE cc_start: 0.7719 (t80) cc_final: 0.7518 (t80) outliers start: 19 outliers final: 15 residues processed: 180 average time/residue: 0.2643 time to fit residues: 68.8996 Evaluate side-chains 177 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 822 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13411 Z= 0.251 Angle : 0.558 9.887 18199 Z= 0.288 Chirality : 0.046 0.284 2052 Planarity : 0.004 0.058 2291 Dihedral : 7.309 110.822 1977 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.57 % Allowed : 11.30 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1606 helix: 0.78 (0.20), residues: 696 sheet: -1.04 (0.38), residues: 201 loop : -1.53 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 206 HIS 0.004 0.001 HIS B 359 PHE 0.017 0.001 PHE A 788 TYR 0.023 0.002 TYR A 573 ARG 0.005 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: A 270 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.7996 (t80) REVERT: B 635 ILE cc_start: 0.9012 (mt) cc_final: 0.8617 (mt) REVERT: B 641 PRO cc_start: 0.8027 (Cg_exo) cc_final: 0.7776 (Cg_endo) REVERT: B 729 PHE cc_start: 0.7878 (t80) cc_final: 0.7591 (t80) outliers start: 22 outliers final: 18 residues processed: 173 average time/residue: 0.2536 time to fit residues: 63.6743 Evaluate side-chains 176 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 161 optimal weight: 0.0970 chunk 148 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 99 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13411 Z= 0.157 Angle : 0.509 9.616 18199 Z= 0.264 Chirality : 0.044 0.268 2052 Planarity : 0.004 0.052 2291 Dihedral : 7.103 110.528 1977 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.50 % Allowed : 11.52 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1606 helix: 1.00 (0.20), residues: 693 sheet: -1.07 (0.37), residues: 203 loop : -1.44 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 299 HIS 0.004 0.001 HIS B 359 PHE 0.016 0.001 PHE A 788 TYR 0.014 0.001 TYR A 573 ARG 0.003 0.000 ARG A 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 1.522 Fit side-chains REVERT: A 270 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.7962 (t80) REVERT: B 270 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7896 (t80) REVERT: B 394 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7710 (mp) REVERT: B 635 ILE cc_start: 0.9022 (mt) cc_final: 0.8629 (mt) REVERT: B 641 PRO cc_start: 0.8086 (Cg_exo) cc_final: 0.7842 (Cg_endo) outliers start: 21 outliers final: 18 residues processed: 172 average time/residue: 0.2475 time to fit residues: 62.2900 Evaluate side-chains 175 residues out of total 1417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 500 ASP Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 480 ASP Chi-restraints excluded: chain B residue 544 ARG Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.0020 chunk 128 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 16 optimal weight: 0.0270 chunk 23 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 overall best weight: 0.3846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.104650 restraints weight = 19776.583| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.25 r_work: 0.2994 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13411 Z= 0.157 Angle : 0.505 9.793 18199 Z= 0.261 Chirality : 0.044 0.270 2052 Planarity : 0.004 0.048 2291 Dihedral : 7.055 110.487 1977 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.65 % Allowed : 11.37 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.21), residues: 1606 helix: 1.17 (0.20), residues: 693 sheet: -1.04 (0.37), residues: 203 loop : -1.38 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 299 HIS 0.004 0.001 HIS B 359 PHE 0.016 0.001 PHE A 788 TYR 0.014 0.001 TYR A 573 ARG 0.002 0.000 ARG B 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2680.45 seconds wall clock time: 49 minutes 24.72 seconds (2964.72 seconds total)