Starting phenix.real_space_refine on Wed Aug 7 07:47:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpu_37724/08_2024/8wpu_37724.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpu_37724/08_2024/8wpu_37724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpu_37724/08_2024/8wpu_37724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpu_37724/08_2024/8wpu_37724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpu_37724/08_2024/8wpu_37724.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpu_37724/08_2024/8wpu_37724.cif" } resolution = 3.1 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= 0.007 sd= 0.041 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 101 5.16 5 C 12107 2.51 5 N 3124 2.21 5 O 3450 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 234": "OD1" <-> "OD2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 451": "OD1" <-> "OD2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 14": "OE1" <-> "OE2" Residue "G ASP 85": "OD1" <-> "OD2" Residue "G ASP 124": "OD1" <-> "OD2" Residue "G PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 233": "OD1" <-> "OD2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 323": "OD1" <-> "OD2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 18794 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 6178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6178 Classifications: {'peptide': 808} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 31, 'TRANS': 776} Chain breaks: 3 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 18, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 172 Chain: "A" Number of atoms: 6169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6169 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 31, 'TRANS': 771} Chain breaks: 3 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 139 Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1619 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 3, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 127 Chain: "C" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2523 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 356 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1643 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "F" 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: "H" 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: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 132 Unusual residues: {' CA': 2, 'CLR': 1, 'NAG': 4, 'PO4': 1, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP B1106 "'] 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: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 118 Unusual residues: {' CA': 2, 'NAG': 5, 'PO4': 1, 'YP4': 1} Inner-chain residues flagged as termini: ['pdbres="TRP A1107 "'] Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 11.19, per 1000 atoms: 0.60 Number of scatterers: 18794 At special positions: 0 Unit cell: (147.66, 120.91, 245.03, 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 S 101 16.00 P 2 15.00 F 6 9.00 O 3450 8.00 N 3124 7.00 C 12107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 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 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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 F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1102 " - " ASN A 261 " " NAG A1103 " - " ASN A 287 " " NAG A1104 " - " ASN A 488 " " NAG A1105 " - " ASN A 468 " " NAG A1106 " - " ASN A 594 " " NAG B1101 " - " ASN B 261 " " NAG B1102 " - " ASN B 287 " " NAG B1103 " - " ASN B 468 " " NAG B1104 " - " ASN B 594 " " NAG F 1 " - " ASN B 541 " " NAG H 1 " - " ASN A 541 " Time building additional restraints: 8.06 Conformation dependent library (CDL) restraints added in 3.7 seconds 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 34 sheets defined 39.1% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'B' and resid 64 through 84 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 115 through 124 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.655A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.504A pdb=" N SER B 175 " --> pdb=" O ARG B 172 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 176 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 removed outlier: 4.024A pdb=" N THR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.865A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 272 through 287 Proline residue: B 278 - end of helix Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.929A pdb=" N PHE B 333 " --> pdb=" O GLY B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.542A pdb=" N VAL B 404 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 436 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.828A pdb=" N VAL B 455 " --> pdb=" O ILE B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 525 through 528 Processing helix chain 'B' and resid 612 through 637 Processing helix chain 'B' and resid 642 through 646 removed outlier: 3.999A pdb=" N ALA B 645 " --> pdb=" O ILE B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 665 removed outlier: 3.673A pdb=" N TYR B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 653 " --> pdb=" O GLU B 649 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 673 through 699 removed outlier: 5.035A pdb=" N GLN B 681 " --> pdb=" O CYS B 677 " (cutoff:3.500A) Proline residue: B 682 - end of helix removed outlier: 3.737A pdb=" N CYS B 694 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 746 removed outlier: 3.583A pdb=" N CYS B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 793 removed outlier: 4.036A pdb=" N LEU B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 793 " --> pdb=" O PHE B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 826 removed outlier: 3.545A pdb=" N PHE B 806 " --> pdb=" O ASN B 802 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 836 through 861 removed outlier: 3.633A pdb=" N CYS B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LYS B 856 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 859 " --> pdb=" O ASN B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 868 removed outlier: 4.469A pdb=" N ARG B 866 " --> pdb=" O LYS B 863 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 868 " --> pdb=" O SER B 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 84 Processing helix chain 'A' and resid 103 through 115 Processing helix chain 'A' and resid 115 through 124 Processing helix chain 'A' and resid 146 through 158 removed outlier: 3.813A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.560A pdb=" N ASN A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 204 removed outlier: 4.243A pdb=" N GLN A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.786A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 272 through 286 Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.526A pdb=" N SER A 403 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 404 " --> pdb=" O ILE A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.564A pdb=" N VAL A 455 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 525 through 528 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 610 through 637 Processing helix chain 'A' and resid 640 through 646 removed outlier: 3.926A pdb=" N THR A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 664 Processing helix chain 'A' and resid 665 through 668 Processing helix chain 'A' and resid 674 through 679 Processing helix chain 'A' and resid 680 through 706 removed outlier: 3.590A pdb=" N PHE A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL A 702 " --> pdb=" O LYS A 698 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 744 removed outlier: 3.672A pdb=" N LEU A 726 " --> pdb=" O ASN A 722 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLN A 735 " --> pdb=" O CYS A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 794 removed outlier: 3.903A pdb=" N LEU A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 802 Processing helix chain 'A' and resid 803 through 821 Processing helix chain 'A' and resid 821 through 828 Processing helix chain 'A' and resid 831 through 862 removed outlier: 3.960A pdb=" N GLU A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 33 removed outlier: 3.767A pdb=" N GLU G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 50 removed outlier: 3.926A pdb=" N GLY G 45 " --> pdb=" O ASP G 42 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS G 46 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER G 47 " --> pdb=" O SER G 44 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 50 " --> pdb=" O SER G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 130 Processing helix chain 'G' and resid 146 through 154 removed outlier: 4.279A pdb=" N ALA G 150 " --> pdb=" O GLN G 146 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 184 through 202 removed outlier: 3.983A pdb=" N PHE G 192 " --> pdb=" O ARG G 188 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG G 194 " --> pdb=" O LYS G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 243 removed outlier: 3.798A pdb=" N ASP G 233 " --> pdb=" O ASN G 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 removed outlier: 3.695A pdb=" N ASP C 5 " --> pdb=" O GLN C 1 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 23 removed outlier: 3.768A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA C 21 " --> pdb=" O GLN C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 4.104A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 16 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 30 through 44 removed outlier: 3.799A pdb=" N ASP D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ALA D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 61 through 65 Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.518A pdb=" N TYR B 95 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 34 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N PHE B 98 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY B 36 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE B 33 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA B 140 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 164 through 166 removed outlier: 5.879A pdb=" N GLN B 164 " --> pdb=" O LEU B 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.946A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 319 through 322 removed outlier: 6.574A pdb=" N TYR B 489 " --> pdb=" O TYR B 510 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR B 510 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 491 " --> pdb=" O VAL B 508 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 469 through 470 removed outlier: 3.895A pdb=" N PHE B 469 " --> pdb=" O VAL B 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 550 through 554 Processing sheet with id=AA7, first strand: chain 'B' and resid 572 through 573 Processing sheet with id=AA8, first strand: chain 'B' and resid 590 through 591 Processing sheet with id=AA9, first strand: chain 'B' and resid 602 through 604 removed outlier: 5.534A pdb=" N GLU B 602 " --> pdb=" O ILE B 761 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 763 " --> pdb=" O GLU B 602 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU B 604 " --> pdb=" O ILE B 763 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.184A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU A 34 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE A 98 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY A 36 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE A 33 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A 140 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 164 through 166 removed outlier: 5.735A pdb=" N GLN A 164 " --> pdb=" O LEU A 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.772A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TRP A 208 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N VAL A 268 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY A 210 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE A 270 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 212 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 318 through 322 removed outlier: 6.356A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 468 through 470 Processing sheet with id=AB6, first strand: chain 'A' and resid 550 through 554 Processing sheet with id=AB7, first strand: chain 'A' and resid 572 through 573 removed outlier: 3.641A pdb=" N TYR A 573 " --> pdb=" O ASN A 583 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AB9, first strand: chain 'A' and resid 749 through 753 Processing sheet with id=AC1, first strand: chain 'G' and resid 70 through 76 removed outlier: 7.129A pdb=" N ARG G 35 " --> pdb=" O ALA G 105 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE G 107 " --> pdb=" O ARG G 35 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU G 37 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL G 109 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU G 39 " --> pdb=" O VAL G 109 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ASP G 111 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL G 139 " --> pdb=" O TYR G 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.666A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.694A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.627A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.522A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 191 through 192 removed outlier: 3.667A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.988A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 254 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.564A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP C 303 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 315 through 317 Processing sheet with id=AD1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.528A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.528A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 45 through 50 removed outlier: 7.034A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AD5, first strand: chain 'E' and resid 134 through 136 Processing sheet with id=AD6, first strand: chain 'E' and resid 142 through 148 removed outlier: 3.875A pdb=" N VAL E 143 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE E 145 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 199 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 174 through 178 removed outlier: 5.062A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 799 hydrogen bonds defined for protein. 2235 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: 6.66 Time building geometry restraints manager: 8.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3169 1.32 - 1.45: 5376 1.45 - 1.57: 10568 1.57 - 1.69: 0 1.69 - 1.81: 125 Bond restraints: 19238 Sorted by residual: bond pdb=" N ARG B 69 " pdb=" CA ARG B 69 " ideal model delta sigma weight residual 1.459 1.383 0.076 1.17e-02 7.31e+03 4.17e+01 bond pdb=" CA LYS A 805 " pdb=" C LYS A 805 " ideal model delta sigma weight residual 1.524 1.446 0.078 1.26e-02 6.30e+03 3.79e+01 bond pdb=" CA ARG B 69 " pdb=" C ARG B 69 " ideal model delta sigma weight residual 1.524 1.459 0.066 1.24e-02 6.50e+03 2.79e+01 bond pdb=" C ASP C 246 " pdb=" N ASP C 247 " ideal model delta sigma weight residual 1.334 1.275 0.059 1.24e-02 6.50e+03 2.27e+01 bond pdb=" CA ARG A 795 " pdb=" C ARG A 795 " ideal model delta sigma weight residual 1.523 1.462 0.060 1.37e-02 5.33e+03 1.94e+01 ... (remaining 19233 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.85: 320 105.85 - 112.89: 10337 112.89 - 119.92: 6297 119.92 - 126.96: 9031 126.96 - 134.00: 224 Bond angle restraints: 26209 Sorted by residual: angle pdb=" N ARG B 69 " pdb=" CA ARG B 69 " pdb=" C ARG B 69 " ideal model delta sigma weight residual 110.97 102.81 8.16 1.09e+00 8.42e-01 5.61e+01 angle pdb=" CA PRO B 89 " pdb=" N PRO B 89 " pdb=" CD PRO B 89 " ideal model delta sigma weight residual 112.00 105.58 6.42 1.40e+00 5.10e-01 2.10e+01 angle pdb=" O ILE B 599 " pdb=" C ILE B 599 " pdb=" N ALA B 600 " ideal model delta sigma weight residual 122.97 118.79 4.18 1.07e+00 8.73e-01 1.53e+01 angle pdb=" N ILE A 409 " pdb=" CA ILE A 409 " pdb=" C ILE A 409 " ideal model delta sigma weight residual 113.71 110.13 3.58 9.50e-01 1.11e+00 1.42e+01 angle pdb=" C ARG A 795 " pdb=" CA ARG A 795 " pdb=" CB ARG A 795 " ideal model delta sigma weight residual 110.38 102.80 7.58 2.04e+00 2.40e-01 1.38e+01 ... (remaining 26204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.77: 10920 31.77 - 63.53: 475 63.53 - 95.30: 29 95.30 - 127.06: 7 127.06 - 158.83: 2 Dihedral angle restraints: 11433 sinusoidal: 4313 harmonic: 7120 Sorted by residual: dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 765 " pdb=" CB CYS A 765 " ideal model delta sinusoidal sigma weight residual 93.00 -178.87 -88.13 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS B 585 " pdb=" SG CYS B 585 " pdb=" SG CYS B 598 " pdb=" CB CYS B 598 " ideal model delta sinusoidal sigma weight residual 93.00 159.96 -66.96 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS B 546 " pdb=" SG CYS B 546 " pdb=" SG CYS B 565 " pdb=" CB CYS B 565 " ideal model delta sinusoidal sigma weight residual -86.00 -139.29 53.29 1 1.00e+01 1.00e-02 3.86e+01 ... (remaining 11430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2557 0.058 - 0.115: 425 0.115 - 0.173: 39 0.173 - 0.231: 1 0.231 - 0.288: 3 Chirality restraints: 3025 Sorted by residual: chirality pdb=" CB ILE B 741 " pdb=" CA ILE B 741 " pdb=" CG1 ILE B 741 " pdb=" CG2 ILE B 741 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 541 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA YP4 A1110 " pdb=" N YP4 A1110 " pdb=" CB YP4 A1110 " pdb=" C1 YP4 A1110 " both_signs ideal model delta sigma weight residual False -2.41 -2.65 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3022 not shown) Planarity restraints: 3322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 88 " 0.088 5.00e-02 4.00e+02 1.30e-01 2.72e+01 pdb=" N PRO B 89 " -0.225 5.00e-02 4.00e+02 pdb=" CA PRO B 89 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO B 89 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 804 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.87e+00 pdb=" C ALA A 804 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA A 804 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS A 805 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 245 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C SER C 245 " 0.038 2.00e-02 2.50e+03 pdb=" O SER C 245 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP C 246 " -0.013 2.00e-02 2.50e+03 ... (remaining 3319 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 667 2.71 - 3.26: 19065 3.26 - 3.81: 31260 3.81 - 4.35: 38232 4.35 - 4.90: 65494 Nonbonded interactions: 154718 Sorted by model distance: nonbonded pdb=" O ASP A 570 " pdb=" OG SER A 591 " model vdw 2.163 3.040 nonbonded pdb=" OH TYR G 212 " pdb=" OD1 ASP G 233 " model vdw 2.201 3.040 nonbonded pdb=" O ALA B 548 " pdb=" OG SER B 574 " model vdw 2.204 3.040 nonbonded pdb=" O4 NAG A1106 " pdb=" O7 NAG A1106 " model vdw 2.212 3.040 nonbonded pdb=" O SER A 794 " pdb=" OG SER A 794 " model vdw 2.225 3.040 ... (remaining 154713 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 20 through 48 or (resid 49 and (name N or name CA or name \ C or name O or name CB )) or resid 50 through 58 or (resid 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 or (resid 61 and (name N or n \ ame CA or name C or name O or name CB )) or resid 62 through 123 or (resid 124 t \ hrough 125 and (name N or name CA or name C or name O or name CB )) or resid 131 \ through 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 230 or (resid 231 and (name N or name CA or name C or n \ ame O or name CB )) or resid 232 through 252 or (resid 253 and (name N or name C \ A or name C or name O or name CB )) or resid 254 through 269 or (resid 270 and ( \ name N or name CA or name C or name O or name CB )) or resid 271 through 296 or \ (resid 297 through 298 and (name N or name CA or name C or name O or name CB )) \ or resid 299 through 393 or (resid 394 and (name N or name CA or name C or name \ O or name CB )) or resid 395 through 432 or (resid 433 and (name N or name CA or \ name C or name O or name CB )) or resid 434 through 450 or (resid 451 and (name \ N or name CA or name C or name O or name CB )) or resid 452 through 454 or (res \ id 455 through 457 and (name N or name CA or name C or name O or name CB )) or r \ esid 458 through 461 or (resid 462 and (name N or name CA or name C or name O or \ name CB )) or resid 463 through 505 or (resid 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 518 or (resid 519 and (name N o \ r name CA or name C or name O or name CB )) or resid 520 through 525 or (resid 5 \ 26 and (name N or name CA or name C or name O or name CB )) or resid 527 through \ 543 or (resid 544 and (name N or name CA or name C or name O or name CB )) or r \ esid 545 through 551 or (resid 552 and (name N or name CA or name C or name O or \ name CB )) or resid 553 through 575 or (resid 576 and (name N or name CA or nam \ e C or name O or name CB )) or resid 577 or (resid 578 through 579 and (name N o \ r name CA or name C or name O or name CB )) or resid 580 through 583 or (resid 5 \ 84 and (name N or name CA or name C or name O or name CB )) or resid 585 through \ 586 or (resid 587 through 588 and (name N or name CA or name C or name O or nam \ e CB )) or resid 589 through 591 or (resid 592 through 593 and (name N or name C \ A or name C or name O or name CB )) or resid 594 through 635 or (resid 636 throu \ gh 637 and (name N or name CA or name C or name O or name CB )) or resid 638 thr \ ough 641 or (resid 642 and (name N or name CA or name C or name O or name CB )) \ or resid 643 through 664 or (resid 665 and (name N or name CA or name C or name \ O or name CB )) or resid 666 through 673 or (resid 674 and (name N or name CA or \ name C or name O or name CB )) or resid 675 through 704 or (resid 705 and (name \ N or name CA or name C or name O or name CB )) or resid 719 through 723 or (res \ id 724 and (name N or name CA or name C or name O or name CB )) or resid 725 or \ (resid 726 and (name N or name CA or name C or name O or name CB )) or resid 727 \ through 770 or (resid 771 through 772 and (name N or name CA or name C or name \ O or name CB )) or resid 773 through 793 or (resid 794 and (name N or name CA or \ name C or name O or name CB )) or resid 795 through 802 or (resid 803 through 8 \ 04 and (name N or name CA or name C or name O or name CB )) or resid 805 through \ 809 or (resid 810 and (name N or name CA or name C or name O or name CB )) or r \ esid 811 through 862 or (resid 863 and (name N or name CA or name C or name O or \ name CB )) or resid 864 through 865 or resid 1102 through 1105 or resid 1107 th \ rough 1108)) selection = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 28 or (resid 29 and (name N or nam \ e CA or name C or name O or name CB )) or resid 30 through 131 or (resid 132 thr \ ough 135 and (name N or name CA or name C or name O or name CB )) or resid 136 t \ hrough 322 or (resid 323 through 324 and (name N or name CA or name C or name O \ or name CB )) or resid 325 through 348 or (resid 349 and (name N or name CA or n \ ame C or name O or name CB )) or resid 350 through 360 or (resid 361 and (name N \ or name CA or name C or name O or name CB )) or (resid 392 and (name N or name \ CA or name C or name O or name CB )) or resid 393 through 395 or (resid 396 and \ (name N or name CA or name C or name O or name CB )) or resid 397 through 404 or \ (resid 405 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 6 through 445 or (resid 446 and (name N or name CA or name C or name O or name C \ B )) or resid 447 through 452 or (resid 453 through 457 and (name N or name CA o \ r name C or name O or name CB )) or resid 458 through 475 or (resid 476 and (nam \ e N or name CA or name C or name O or name CB )) or resid 477 through 480 or (re \ sid 481 and (name N or name CA or name C or name O or name CB )) or resid 482 th \ rough 512 or (resid 513 and (name N or name CA or name C or name O or name CB )) \ or resid 514 through 516 or (resid 517 and (name N or name CA or name C or name \ O or name CB )) or resid 518 through 535 or (resid 536 and (name N or name CA o \ r name C or name O or name CB )) or resid 537 through 603 or (resid 604 and (nam \ e N or name CA or name C or name O or name CB )) or resid 605 through 609 or (re \ sid 610 and (name N or name CA or name C or name O or name CB )) or resid 611 th \ rough 621 or (resid 622 and (name N or name CA or name C or name O or name CB )) \ or resid 623 through 624 or (resid 625 and (name N or name CA or name C or name \ O or name CB )) or resid 626 through 660 or (resid 661 and (name N or name CA o \ r name C or name O or name CB )) or resid 662 through 670 or (resid 671 and (nam \ e N or name CA or name C or name O or name CB )) or resid 672 through 705 or (re \ sid 719 and (name N or name CA or name C or name O or name CB )) or resid 720 th \ rough 729 or (resid 730 and (name N or name CA or name C or name O or name CB )) \ or resid 731 through 732 or (resid 733 through 734 and (name N or name CA or na \ me C or name O or name CB )) or resid 735 through 736 or (resid 737 and (name N \ or name CA or name C or name O or name CB )) or resid 738 or (resid 739 and (nam \ e N or name CA or name C or name O or name CB )) or resid 740 through 758 or (re \ sid 759 and (name N or name CA or name C or name O or name CB )) or resid 760 th \ rough 792 or (resid 793 through 794 and (name N or name CA or name C or name O o \ r name CB )) or resid 795 through 830 or (resid 831 and (name N or name CA or na \ me C or name O or name CB )) or resid 832 through 865 or resid 1101 through 1104 \ or resid 1106 through 1107)) } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 18.810 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: 0.000 Extract box with map and model: 1.140 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 54.370 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 19238 Z= 0.270 Angle : 0.588 9.205 26209 Z= 0.318 Chirality : 0.043 0.288 3025 Planarity : 0.004 0.130 3311 Dihedral : 16.874 158.829 6776 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 28.01 % Favored : 71.99 % 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 (0.17), residues: 2423 helix: 0.72 (0.18), residues: 830 sheet: -1.22 (0.26), residues: 412 loop : -0.96 (0.19), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 608 HIS 0.006 0.001 HIS C 142 PHE 0.030 0.001 PHE G 192 TYR 0.021 0.001 TYR E 223 ARG 0.008 0.000 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 ASP cc_start: 0.8307 (m-30) cc_final: 0.7913 (t0) REVERT: G 46 LYS cc_start: 0.7992 (mttt) cc_final: 0.7761 (mttt) REVERT: G 244 ASN cc_start: 0.8386 (t0) cc_final: 0.7787 (t0) REVERT: C 264 TYR cc_start: 0.8000 (m-10) cc_final: 0.7698 (m-80) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3050 time to fit residues: 114.9802 Evaluate side-chains 236 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 0.8980 chunk 183 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 73 optimal weight: 0.0170 chunk 115 optimal weight: 0.2980 chunk 141 optimal weight: 0.9980 chunk 219 optimal weight: 4.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 HIS A 463 HIS A 466 HIS A 735 GLN A 802 ASN G 123 ASN C 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19238 Z= 0.190 Angle : 0.541 7.971 26209 Z= 0.286 Chirality : 0.043 0.202 3025 Planarity : 0.004 0.077 3311 Dihedral : 8.624 153.993 2979 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.39 % Allowed : 24.84 % Favored : 71.77 % 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 (0.17), residues: 2423 helix: 0.88 (0.18), residues: 844 sheet: -1.21 (0.25), residues: 448 loop : -0.98 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 82 HIS 0.006 0.001 HIS E 35 PHE 0.015 0.001 PHE A 589 TYR 0.021 0.001 TYR E 223 ARG 0.006 0.000 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 247 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 659 LEU cc_start: 0.8725 (mt) cc_final: 0.8438 (mm) REVERT: C 142 HIS cc_start: 0.7738 (OUTLIER) cc_final: 0.6405 (t70) REVERT: C 264 TYR cc_start: 0.8223 (m-10) cc_final: 0.7887 (m-80) REVERT: E 204 ILE cc_start: 0.3929 (OUTLIER) cc_final: 0.3502 (tt) REVERT: E 223 TYR cc_start: 0.7377 (t80) cc_final: 0.7156 (t80) outliers start: 63 outliers final: 25 residues processed: 288 average time/residue: 0.3030 time to fit residues: 132.8612 Evaluate side-chains 258 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 231 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 182 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 237 optimal weight: 0.0370 chunk 196 optimal weight: 1.9990 chunk 218 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 176 optimal weight: 0.7980 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN A 260 GLN C 259 GLN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19238 Z= 0.234 Angle : 0.530 9.236 26209 Z= 0.279 Chirality : 0.043 0.205 3025 Planarity : 0.004 0.056 3311 Dihedral : 7.956 152.273 2979 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.35 % Allowed : 23.76 % Favored : 71.88 % 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: -0.53 (0.17), residues: 2423 helix: 0.94 (0.18), residues: 846 sheet: -1.10 (0.25), residues: 444 loop : -0.97 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 PHE 0.016 0.001 PHE B 806 TYR 0.024 0.001 TYR E 223 ARG 0.006 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 244 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 589 PHE cc_start: 0.8545 (m-80) cc_final: 0.8278 (m-80) REVERT: B 686 ILE cc_start: 0.7221 (pt) cc_final: 0.6802 (mm) REVERT: G 142 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7475 (m-10) REVERT: G 148 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.5324 (pt) REVERT: G 151 GLU cc_start: 0.3643 (OUTLIER) cc_final: 0.3357 (tp30) REVERT: C 142 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.6805 (t70) REVERT: C 262 MET cc_start: 0.7095 (tpp) cc_final: 0.6579 (tpp) REVERT: C 264 TYR cc_start: 0.8223 (m-10) cc_final: 0.7918 (m-80) REVERT: E 204 ILE cc_start: 0.3887 (OUTLIER) cc_final: 0.3441 (tt) REVERT: E 223 TYR cc_start: 0.7402 (t80) cc_final: 0.7144 (t80) outliers start: 81 outliers final: 42 residues processed: 301 average time/residue: 0.2999 time to fit residues: 138.9855 Evaluate side-chains 278 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 231 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 839 ILE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 220 optimal weight: 3.9990 chunk 233 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19238 Z= 0.282 Angle : 0.543 10.667 26209 Z= 0.287 Chirality : 0.043 0.211 3025 Planarity : 0.004 0.044 3311 Dihedral : 7.524 151.848 2979 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.95 % Allowed : 23.33 % Favored : 71.72 % 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: -0.56 (0.17), residues: 2423 helix: 0.95 (0.18), residues: 841 sheet: -1.09 (0.25), residues: 445 loop : -1.03 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.007 0.001 HIS E 35 PHE 0.021 0.002 PHE A 789 TYR 0.028 0.001 TYR E 223 ARG 0.008 0.000 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 239 time to evaluate : 2.091 Fit side-chains revert: symmetry clash REVERT: B 686 ILE cc_start: 0.7168 (pt) cc_final: 0.6771 (mm) REVERT: A 425 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.7732 (m-10) REVERT: G 23 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8261 (mt) REVERT: G 142 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7537 (m-10) REVERT: G 148 LEU cc_start: 0.5676 (OUTLIER) cc_final: 0.5445 (pt) REVERT: G 151 GLU cc_start: 0.3761 (OUTLIER) cc_final: 0.3495 (tp30) REVERT: C 44 GLN cc_start: 0.7117 (pp30) cc_final: 0.6888 (pp30) REVERT: C 264 TYR cc_start: 0.8231 (m-10) cc_final: 0.7986 (m-80) REVERT: E 204 ILE cc_start: 0.3921 (OUTLIER) cc_final: 0.3459 (tt) REVERT: E 223 TYR cc_start: 0.7372 (t80) cc_final: 0.7159 (t80) outliers start: 92 outliers final: 56 residues processed: 305 average time/residue: 0.3001 time to fit residues: 141.9268 Evaluate side-chains 294 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 232 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 209 HIS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 103 CYS Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 174 optimal weight: 0.0030 chunk 96 optimal weight: 0.5980 chunk 199 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN B 476 GLN A 179 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 19238 Z= 0.377 Angle : 0.592 10.155 26209 Z= 0.313 Chirality : 0.045 0.234 3025 Planarity : 0.004 0.049 3311 Dihedral : 7.180 147.620 2979 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.11 % Allowed : 24.14 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2423 helix: 0.76 (0.18), residues: 855 sheet: -1.16 (0.25), residues: 441 loop : -1.11 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.008 0.001 HIS E 35 PHE 0.026 0.002 PHE A 605 TYR 0.030 0.002 TYR E 223 ARG 0.009 0.001 ARG C 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 238 time to evaluate : 2.259 Fit side-chains revert: symmetry clash REVERT: B 603 ILE cc_start: 0.8865 (mm) cc_final: 0.8638 (mt) REVERT: B 686 ILE cc_start: 0.7383 (pt) cc_final: 0.6941 (mm) REVERT: A 425 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7780 (m-10) REVERT: A 680 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7868 (mtp180) REVERT: G 8 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: G 98 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7218 (tm-30) REVERT: G 142 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7606 (m-10) REVERT: G 151 GLU cc_start: 0.4138 (OUTLIER) cc_final: 0.3730 (tp30) REVERT: G 244 ASN cc_start: 0.8414 (t0) cc_final: 0.7760 (t0) REVERT: C 44 GLN cc_start: 0.7105 (pp30) cc_final: 0.6838 (pp30) REVERT: C 264 TYR cc_start: 0.8258 (m-10) cc_final: 0.8034 (m-80) REVERT: C 289 TYR cc_start: 0.8149 (m-80) cc_final: 0.7933 (m-80) outliers start: 95 outliers final: 65 residues processed: 309 average time/residue: 0.2915 time to fit residues: 142.2898 Evaluate side-chains 304 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 234 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 151 GLU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 209 HIS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 234 optimal weight: 0.0870 chunk 194 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN A 260 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19238 Z= 0.203 Angle : 0.522 7.031 26209 Z= 0.276 Chirality : 0.042 0.217 3025 Planarity : 0.004 0.046 3311 Dihedral : 6.647 131.755 2979 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.25 % Allowed : 24.95 % Favored : 70.81 % 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: -0.59 (0.17), residues: 2423 helix: 0.97 (0.18), residues: 841 sheet: -1.15 (0.25), residues: 446 loop : -1.05 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.006 0.001 HIS C 142 PHE 0.026 0.001 PHE G 192 TYR 0.023 0.001 TYR E 223 ARG 0.007 0.000 ARG C 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 240 time to evaluate : 2.285 Fit side-chains revert: symmetry clash REVERT: B 603 ILE cc_start: 0.8845 (mm) cc_final: 0.8607 (tp) REVERT: B 686 ILE cc_start: 0.7209 (pt) cc_final: 0.6813 (mm) REVERT: A 425 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7803 (m-10) REVERT: A 771 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6878 (tpp) REVERT: G 8 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: G 23 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8274 (mt) REVERT: G 53 MET cc_start: 0.5196 (mtm) cc_final: 0.4807 (ttt) REVERT: G 244 ASN cc_start: 0.8377 (t0) cc_final: 0.7770 (t0) REVERT: C 44 GLN cc_start: 0.6921 (pp30) cc_final: 0.6633 (pp30) REVERT: C 234 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8483 (t80) REVERT: C 264 TYR cc_start: 0.8177 (m-10) cc_final: 0.7914 (m-80) REVERT: E 204 ILE cc_start: 0.3964 (OUTLIER) cc_final: 0.3514 (tt) outliers start: 79 outliers final: 55 residues processed: 295 average time/residue: 0.2921 time to fit residues: 133.9098 Evaluate side-chains 290 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 229 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 19238 Z= 0.473 Angle : 0.638 7.342 26209 Z= 0.338 Chirality : 0.047 0.238 3025 Planarity : 0.005 0.052 3311 Dihedral : 6.879 124.207 2979 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.43 % Allowed : 24.14 % Favored : 70.43 % 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: -0.85 (0.17), residues: 2423 helix: 0.68 (0.18), residues: 849 sheet: -1.28 (0.25), residues: 442 loop : -1.16 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 530 HIS 0.008 0.001 HIS A 41 PHE 0.027 0.002 PHE G 192 TYR 0.026 0.002 TYR E 223 ARG 0.007 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 233 time to evaluate : 2.113 Fit side-chains revert: symmetry clash REVERT: B 251 GLU cc_start: 0.7483 (pt0) cc_final: 0.7267 (pt0) REVERT: B 686 ILE cc_start: 0.7415 (pt) cc_final: 0.7007 (mm) REVERT: A 425 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7882 (m-10) REVERT: A 680 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7877 (mtp180) REVERT: G 23 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8301 (mt) REVERT: G 98 GLN cc_start: 0.7752 (tm-30) cc_final: 0.7319 (tm-30) REVERT: G 142 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7629 (m-10) REVERT: G 244 ASN cc_start: 0.8428 (t0) cc_final: 0.7770 (t0) REVERT: C 44 GLN cc_start: 0.6973 (pp30) cc_final: 0.6647 (pp30) REVERT: C 264 TYR cc_start: 0.8241 (m-10) cc_final: 0.8014 (m-80) REVERT: C 289 TYR cc_start: 0.8152 (m-80) cc_final: 0.7918 (m-80) REVERT: E 100 ILE cc_start: 0.8282 (tp) cc_final: 0.7930 (tt) REVERT: E 214 VAL cc_start: 0.7870 (m) cc_final: 0.7525 (p) outliers start: 101 outliers final: 73 residues processed: 312 average time/residue: 0.3069 time to fit residues: 150.4762 Evaluate side-chains 304 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 227 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 739 CYS Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 834 SER Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 855 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 71 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 142 PHE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 209 HIS Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 70 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 148 optimal weight: 0.0570 chunk 158 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 183 optimal weight: 0.4980 chunk 212 optimal weight: 0.0070 overall best weight: 0.1674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19238 Z= 0.156 Angle : 0.525 8.957 26209 Z= 0.276 Chirality : 0.042 0.279 3025 Planarity : 0.004 0.045 3311 Dihedral : 6.271 109.851 2979 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.82 % Allowed : 25.65 % Favored : 70.54 % 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: -0.59 (0.17), residues: 2423 helix: 0.94 (0.18), residues: 846 sheet: -1.23 (0.25), residues: 439 loop : -1.01 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 82 HIS 0.006 0.001 HIS C 142 PHE 0.026 0.001 PHE G 192 TYR 0.024 0.001 TYR E 223 ARG 0.007 0.000 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 237 time to evaluate : 2.096 Fit side-chains revert: symmetry clash REVERT: B 251 GLU cc_start: 0.7335 (pt0) cc_final: 0.7111 (pt0) REVERT: B 589 PHE cc_start: 0.8483 (m-80) cc_final: 0.8224 (m-80) REVERT: B 686 ILE cc_start: 0.7184 (pt) cc_final: 0.6816 (mm) REVERT: A 159 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8154 (mp) REVERT: A 425 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7760 (m-10) REVERT: G 8 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: G 53 MET cc_start: 0.5169 (mtm) cc_final: 0.4743 (ttt) REVERT: G 244 ASN cc_start: 0.8343 (t0) cc_final: 0.7731 (t0) REVERT: C 44 GLN cc_start: 0.6928 (pp30) cc_final: 0.6612 (pp30) REVERT: C 264 TYR cc_start: 0.8178 (m-10) cc_final: 0.7846 (m-80) REVERT: E 7 SER cc_start: 0.7861 (m) cc_final: 0.7458 (p) REVERT: E 204 ILE cc_start: 0.3907 (OUTLIER) cc_final: 0.3472 (tt) REVERT: E 214 VAL cc_start: 0.7939 (m) cc_final: 0.7590 (p) REVERT: E 223 TYR cc_start: 0.7250 (t80) cc_final: 0.6986 (t80) outliers start: 71 outliers final: 50 residues processed: 284 average time/residue: 0.2874 time to fit residues: 126.4612 Evaluate side-chains 280 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 226 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 216 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19238 Z= 0.341 Angle : 0.578 8.117 26209 Z= 0.305 Chirality : 0.045 0.230 3025 Planarity : 0.004 0.049 3311 Dihedral : 6.383 116.992 2979 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.60 % Allowed : 25.91 % Favored : 70.48 % 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: -0.66 (0.17), residues: 2423 helix: 0.90 (0.18), residues: 845 sheet: -1.26 (0.24), residues: 446 loop : -1.06 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 530 HIS 0.008 0.001 HIS E 35 PHE 0.031 0.002 PHE G 192 TYR 0.027 0.002 TYR E 223 ARG 0.008 0.001 ARG A 752 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 227 time to evaluate : 2.152 Fit side-chains revert: symmetry clash REVERT: B 251 GLU cc_start: 0.7418 (pt0) cc_final: 0.7201 (pt0) REVERT: B 686 ILE cc_start: 0.7403 (pt) cc_final: 0.6999 (mm) REVERT: A 425 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7871 (m-10) REVERT: A 680 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7824 (mtp180) REVERT: G 8 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: G 53 MET cc_start: 0.5197 (mtm) cc_final: 0.4740 (ttt) REVERT: G 244 ASN cc_start: 0.8383 (t0) cc_final: 0.7743 (t0) REVERT: C 44 GLN cc_start: 0.6958 (pp30) cc_final: 0.6632 (pp30) REVERT: C 264 TYR cc_start: 0.8236 (m-10) cc_final: 0.7960 (m-80) REVERT: C 289 TYR cc_start: 0.8147 (m-80) cc_final: 0.7922 (m-80) REVERT: E 100 ILE cc_start: 0.8308 (tp) cc_final: 0.7966 (tt) REVERT: E 214 VAL cc_start: 0.7928 (m) cc_final: 0.7538 (p) REVERT: E 223 TYR cc_start: 0.7373 (t80) cc_final: 0.7166 (t80) outliers start: 67 outliers final: 55 residues processed: 277 average time/residue: 0.2919 time to fit residues: 126.1558 Evaluate side-chains 282 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 224 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 680 ARG Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 241 optimal weight: 0.7980 chunk 221 optimal weight: 0.0970 chunk 191 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 148 optimal weight: 0.0050 chunk 117 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 overall best weight: 0.3370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN ** C 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19238 Z= 0.167 Angle : 0.522 8.946 26209 Z= 0.274 Chirality : 0.042 0.258 3025 Planarity : 0.004 0.047 3311 Dihedral : 5.956 106.488 2979 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.17 % Allowed : 26.34 % Favored : 70.48 % 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: -0.50 (0.17), residues: 2423 helix: 0.98 (0.18), residues: 845 sheet: -1.10 (0.26), residues: 413 loop : -0.97 (0.19), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 82 HIS 0.006 0.001 HIS C 142 PHE 0.027 0.001 PHE G 192 TYR 0.024 0.001 TYR E 223 ARG 0.007 0.000 ARG C 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4846 Ramachandran restraints generated. 2423 Oldfield, 0 Emsley, 2423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 234 time to evaluate : 2.028 Fit side-chains revert: symmetry clash REVERT: B 251 GLU cc_start: 0.7290 (pt0) cc_final: 0.7069 (pt0) REVERT: B 589 PHE cc_start: 0.8494 (m-80) cc_final: 0.8227 (m-80) REVERT: B 686 ILE cc_start: 0.7360 (pt) cc_final: 0.6963 (mm) REVERT: A 159 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8152 (mp) REVERT: A 425 TYR cc_start: 0.8250 (OUTLIER) cc_final: 0.7836 (m-10) REVERT: G 8 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: G 53 MET cc_start: 0.5111 (mtm) cc_final: 0.4747 (ttt) REVERT: G 244 ASN cc_start: 0.8358 (t0) cc_final: 0.7760 (t0) REVERT: C 44 GLN cc_start: 0.6932 (pp30) cc_final: 0.6615 (pp30) REVERT: C 264 TYR cc_start: 0.8095 (m-10) cc_final: 0.7835 (m-80) REVERT: C 292 PHE cc_start: 0.8361 (m-80) cc_final: 0.8141 (m-80) REVERT: E 7 SER cc_start: 0.7832 (m) cc_final: 0.7442 (p) REVERT: E 204 ILE cc_start: 0.4006 (OUTLIER) cc_final: 0.3562 (tt) REVERT: E 214 VAL cc_start: 0.7896 (m) cc_final: 0.7525 (p) REVERT: E 223 TYR cc_start: 0.7195 (t80) cc_final: 0.6928 (t80) outliers start: 59 outliers final: 49 residues processed: 275 average time/residue: 0.2963 time to fit residues: 126.0014 Evaluate side-chains 279 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 226 time to evaluate : 2.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 425 TYR Chi-restraints excluded: chain B residue 426 SER Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 691 CYS Chi-restraints excluded: chain B residue 695 ILE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 812 LEU Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 150 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 425 TYR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain G residue 8 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 142 HIS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.093030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.078236 restraints weight = 45903.545| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.19 r_work: 0.3225 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 19238 Z= 0.483 Angle : 0.638 8.068 26209 Z= 0.338 Chirality : 0.047 0.219 3025 Planarity : 0.005 0.050 3311 Dihedral : 6.395 111.106 2979 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.60 % Allowed : 25.86 % Favored : 70.54 % 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: -0.80 (0.17), residues: 2423 helix: 0.69 (0.18), residues: 854 sheet: -1.27 (0.25), residues: 442 loop : -1.12 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 530 HIS 0.009 0.001 HIS E 35 PHE 0.036 0.002 PHE G 192 TYR 0.030 0.002 TYR E 223 ARG 0.008 0.001 ARG A 752 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4752.02 seconds wall clock time: 91 minutes 28.64 seconds (5488.64 seconds total)