Starting phenix.real_space_refine on Sat Mar 16 09:14:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/03_2024/6n51_0345_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/03_2024/6n51_0345.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/03_2024/6n51_0345_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/03_2024/6n51_0345_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/03_2024/6n51_0345_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/03_2024/6n51_0345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/03_2024/6n51_0345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/03_2024/6n51_0345_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n51_0345/03_2024/6n51_0345_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 164 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 8951 2.51 5 N 2394 2.21 5 O 2614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 574": "NH1" <-> "NH2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 574": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14087 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6075 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 759} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 115 Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 939 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "D" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 931 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 6060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6060 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 757} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'NAG': 2, 'QUS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'NAG': 2, 'QUS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.51, per 1000 atoms: 0.53 Number of scatterers: 14087 At special positions: 0 Unit cell: (96.46, 108.12, 203.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 2614 8.00 N 2394 7.00 C 8951 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.04 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.02 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.02 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.04 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.02 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.02 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " 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 NAG-ASN " NAG A 901 " - " ASN A 210 " " NAG A 902 " - " ASN A 445 " " NAG B 901 " - " ASN B 210 " " NAG B 902 " - " ASN B 445 " Time building additional restraints: 5.52 Conformation dependent library (CDL) restraints added in 2.7 seconds 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 20 sheets defined 37.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'B' and resid 66 through 81 Processing helix chain 'B' and resid 102 through 120 removed outlier: 5.202A pdb=" N ASP B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 164 removed outlier: 3.923A pdb=" N ASN B 160 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 164 " --> pdb=" O ASN B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 224 through 237 removed outlier: 4.257A pdb=" N ALA B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS B 237 " --> pdb=" O ASP B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 258 through 267 removed outlier: 3.925A pdb=" N SER B 266 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N HIS B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 318 through 321 Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.730A pdb=" N PHE B 363 " --> pdb=" O TRP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 418 removed outlier: 3.509A pdb=" N ILE B 401 " --> pdb=" O MET B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 443 removed outlier: 4.093A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 601 removed outlier: 3.641A pdb=" N ALA B 582 " --> pdb=" O PRO B 578 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 583 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 600 " --> pdb=" O PHE B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 612 Processing helix chain 'B' and resid 615 through 633 removed outlier: 3.945A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 668 removed outlier: 4.304A pdb=" N SER B 654 " --> pdb=" O GLY B 650 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 3.923A pdb=" N LEU B 662 " --> pdb=" O SER B 658 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR B 664 " --> pdb=" O SER B 660 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS B 665 " --> pdb=" O ALA B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 673 No H-bonds generated for 'chain 'B' and resid 670 through 673' Processing helix chain 'B' and resid 690 through 714 removed outlier: 3.632A pdb=" N ILE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B 700 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N CYS B 702 " --> pdb=" O PHE B 698 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU B 705 " --> pdb=" O ILE B 701 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 757 Proline residue: B 743 - end of helix removed outlier: 3.941A pdb=" N TYR B 746 " --> pdb=" O THR B 742 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN B 747 " --> pdb=" O PRO B 743 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU B 749 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 752 " --> pdb=" O GLY B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 763 Processing helix chain 'B' and resid 770 through 793 removed outlier: 4.205A pdb=" N ILE B 783 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE B 784 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP B 785 " --> pdb=" O THR B 781 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL B 789 " --> pdb=" O TRP B 785 " (cutoff:3.500A) Proline residue: B 790 - end of helix Processing helix chain 'B' and resid 800 through 815 removed outlier: 4.083A pdb=" N VAL B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 825 removed outlier: 3.568A pdb=" N ILE B 824 " --> pdb=" O PRO B 820 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE B 825 " --> pdb=" O LYS B 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 102 through 120 removed outlier: 5.203A pdb=" N ASP A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 164 removed outlier: 3.923A pdb=" N ASN A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 198 through 208 Processing helix chain 'A' and resid 224 through 237 removed outlier: 4.257A pdb=" N ALA A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS A 237 " --> pdb=" O ASP A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 258 through 267 removed outlier: 3.925A pdb=" N SER A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N HIS A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 293 Processing helix chain 'A' and resid 305 through 307 No H-bonds generated for 'chain 'A' and resid 305 through 307' Processing helix chain 'A' and resid 318 through 321 Processing helix chain 'A' and resid 335 through 341 Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.729A pdb=" N PHE A 363 " --> pdb=" O TRP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 418 removed outlier: 3.510A pdb=" N ILE A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 443 removed outlier: 4.092A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 601 removed outlier: 3.641A pdb=" N ALA A 582 " --> pdb=" O PRO A 578 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 600 " --> pdb=" O PHE A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 615 through 633 removed outlier: 3.945A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 668 removed outlier: 4.304A pdb=" N SER A 654 " --> pdb=" O GLY A 650 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 3.923A pdb=" N LEU A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR A 664 " --> pdb=" O SER A 660 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LYS A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 673 No H-bonds generated for 'chain 'A' and resid 670 through 673' Processing helix chain 'A' and resid 690 through 714 removed outlier: 3.632A pdb=" N ILE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU A 700 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N CYS A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE A 703 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLN A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU A 705 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 757 Proline residue: A 743 - end of helix removed outlier: 3.941A pdb=" N TYR A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN A 747 " --> pdb=" O PRO A 743 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A 749 " --> pdb=" O GLY A 745 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 752 " --> pdb=" O GLY A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 763 Processing helix chain 'A' and resid 770 through 793 removed outlier: 4.205A pdb=" N ILE A 783 " --> pdb=" O TYR A 779 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE A 784 " --> pdb=" O THR A 780 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP A 785 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL A 789 " --> pdb=" O TRP A 785 " (cutoff:3.500A) Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 800 through 815 removed outlier: 4.083A pdb=" N VAL A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 825 removed outlier: 3.568A pdb=" N ILE A 824 " --> pdb=" O PRO A 820 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE A 825 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 29 through 31 removed outlier: 5.572A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= C, first strand: chain 'B' and resid 274 through 276 removed outlier: 6.906A pdb=" N SER B 215 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 324 through 329 removed outlier: 3.548A pdb=" N TRP B 487 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASN B 470 " --> pdb=" O ASN B 483 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASN B 483 " --> pdb=" O ASN B 470 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS B 472 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TYR B 481 " --> pdb=" O LYS B 472 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 520 through 524 Processing sheet with id= F, first strand: chain 'B' and resid 719 through 722 Processing sheet with id= G, first strand: chain 'B' and resid 541 through 545 removed outlier: 3.700A pdb=" N PHE B 544 " --> pdb=" O THR B 548 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 6 through 9 Processing sheet with id= I, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.562A pdb=" N THR C 122 " --> pdb=" O VAL C 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 47 through 49 removed outlier: 3.533A pdb=" N VAL C 121 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 51 through 53 Processing sheet with id= L, first strand: chain 'D' and resid 5 through 9 Processing sheet with id= M, first strand: chain 'D' and resid 12 through 14 removed outlier: 3.576A pdb=" N VAL D 121 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ARG D 40 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N SER D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 29 through 31 removed outlier: 5.572A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 145 through 147 Processing sheet with id= P, first strand: chain 'A' and resid 274 through 276 removed outlier: 6.906A pdb=" N SER A 215 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 324 through 329 removed outlier: 3.548A pdb=" N TRP A 487 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASN A 470 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASN A 483 " --> pdb=" O ASN A 470 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS A 472 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TYR A 481 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 520 through 524 Processing sheet with id= S, first strand: chain 'A' and resid 719 through 722 Processing sheet with id= T, first strand: chain 'A' and resid 541 through 545 removed outlier: 3.700A pdb=" N PHE A 544 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2277 1.31 - 1.43: 3843 1.43 - 1.56: 8093 1.56 - 1.68: 0 1.68 - 1.81: 186 Bond restraints: 14399 Sorted by residual: bond pdb=" CB GLN A 159 " pdb=" CG GLN A 159 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 4.96e+00 bond pdb=" CB GLN B 159 " pdb=" CG GLN B 159 " ideal model delta sigma weight residual 1.520 1.453 0.067 3.00e-02 1.11e+03 4.95e+00 bond pdb=" CB TRP A 359 " pdb=" CG TRP A 359 " ideal model delta sigma weight residual 1.498 1.449 0.049 3.10e-02 1.04e+03 2.49e+00 bond pdb=" CB TRP B 359 " pdb=" CG TRP B 359 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.44e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.06e+00 ... (remaining 14394 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.25: 239 104.25 - 111.70: 6449 111.70 - 119.15: 5136 119.15 - 126.61: 7479 126.61 - 134.06: 218 Bond angle restraints: 19521 Sorted by residual: angle pdb=" C VAL B 499 " pdb=" N TRP B 500 " pdb=" CA TRP B 500 " ideal model delta sigma weight residual 121.54 130.10 -8.56 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C VAL A 499 " pdb=" N TRP A 500 " pdb=" CA TRP A 500 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C TYR A 797 " pdb=" N LYS A 798 " pdb=" CA LYS A 798 " ideal model delta sigma weight residual 122.08 128.35 -6.27 1.47e+00 4.63e-01 1.82e+01 angle pdb=" C TYR B 797 " pdb=" N LYS B 798 " pdb=" CA LYS B 798 " ideal model delta sigma weight residual 122.08 128.34 -6.26 1.47e+00 4.63e-01 1.82e+01 angle pdb=" C SER C 49 " pdb=" N VAL C 50 " pdb=" CA VAL C 50 " ideal model delta sigma weight residual 122.97 119.68 3.29 9.80e-01 1.04e+00 1.13e+01 ... (remaining 19516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.73: 8289 15.73 - 31.46: 287 31.46 - 47.20: 83 47.20 - 62.93: 10 62.93 - 78.66: 12 Dihedral angle restraints: 8681 sinusoidal: 3383 harmonic: 5298 Sorted by residual: dihedral pdb=" CB CYS A 419 " pdb=" SG CYS A 419 " pdb=" SG CYS A 426 " pdb=" CB CYS A 426 " ideal model delta sinusoidal sigma weight residual 93.00 164.98 -71.98 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CB CYS B 419 " pdb=" SG CYS B 419 " pdb=" SG CYS B 426 " pdb=" CB CYS B 426 " ideal model delta sinusoidal sigma weight residual 93.00 164.97 -71.97 1 1.00e+01 1.00e-02 6.63e+01 dihedral pdb=" CA ASN B 222 " pdb=" C ASN B 222 " pdb=" N TYR B 223 " pdb=" CA TYR B 223 " ideal model delta harmonic sigma weight residual 180.00 153.30 26.70 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 8678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1592 0.053 - 0.106: 492 0.106 - 0.159: 94 0.159 - 0.212: 2 0.212 - 0.266: 6 Chirality restraints: 2186 Sorted by residual: chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 210 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 210 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CG LEU B 438 " pdb=" CB LEU B 438 " pdb=" CD1 LEU B 438 " pdb=" CD2 LEU B 438 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2183 not shown) Planarity restraints: 2482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 579 " -0.048 5.00e-02 4.00e+02 7.20e-02 8.30e+00 pdb=" N PRO B 580 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 580 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 580 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 579 " 0.048 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO A 580 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 580 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 580 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 159 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" CD GLN B 159 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN B 159 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN B 159 " -0.014 2.00e-02 2.50e+03 ... (remaining 2479 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3911 2.80 - 3.32: 12771 3.32 - 3.85: 23182 3.85 - 4.37: 26397 4.37 - 4.90: 44403 Nonbonded interactions: 110664 Sorted by model distance: nonbonded pdb=" OG1 THR A 175 " pdb=" O16 QUS A 903 " model vdw 2.274 2.440 nonbonded pdb=" O LEU A 261 " pdb=" OG1 THR A 265 " model vdw 2.284 2.440 nonbonded pdb=" O LEU B 261 " pdb=" OG1 THR B 265 " model vdw 2.284 2.440 nonbonded pdb=" OG1 THR B 175 " pdb=" O16 QUS B 903 " model vdw 2.344 2.440 nonbonded pdb=" O TYR A 629 " pdb=" OG1 THR A 632 " model vdw 2.353 2.440 ... (remaining 110659 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 25 through 826 or resid 901 through 903)) } ncs_group { reference = (chain 'C' and (resid 3 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 116 or (resid 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 through 125)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 4.280 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 38.950 Find NCS groups from input model: 0.840 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:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 14399 Z= 0.370 Angle : 0.840 9.779 19521 Z= 0.457 Chirality : 0.051 0.266 2186 Planarity : 0.006 0.072 2478 Dihedral : 9.676 78.662 5229 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -3.65 (0.16), residues: 1818 helix: -2.52 (0.15), residues: 614 sheet: -2.32 (0.28), residues: 292 loop : -2.33 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 307 HIS 0.011 0.002 HIS A 53 PHE 0.019 0.002 PHE A 399 TYR 0.025 0.002 TYR B 317 ARG 0.022 0.001 ARG A 574 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 ASN cc_start: 0.8935 (p0) cc_final: 0.8600 (p0) REVERT: B 429 MET cc_start: 0.8362 (mpt) cc_final: 0.7838 (mpp) REVERT: B 722 ASP cc_start: 0.8564 (t0) cc_final: 0.8189 (t0) REVERT: C 4 VAL cc_start: 0.9197 (t) cc_final: 0.8995 (p) REVERT: C 22 LEU cc_start: 0.8395 (mt) cc_final: 0.7832 (mm) REVERT: C 45 LYS cc_start: 0.9094 (mttt) cc_final: 0.8843 (pttp) REVERT: C 64 ASP cc_start: 0.8661 (m-30) cc_final: 0.8266 (p0) REVERT: C 83 LEU cc_start: 0.9181 (tp) cc_final: 0.8799 (tp) REVERT: C 109 ASP cc_start: 0.9350 (t0) cc_final: 0.8827 (t70) REVERT: D 6 LEU cc_start: 0.8241 (mt) cc_final: 0.7786 (mt) REVERT: D 22 LEU cc_start: 0.8285 (mt) cc_final: 0.7753 (mm) REVERT: D 83 LEU cc_start: 0.9217 (tp) cc_final: 0.8802 (tp) REVERT: D 109 ASP cc_start: 0.9485 (t0) cc_final: 0.9173 (t0) REVERT: A 106 LEU cc_start: 0.9525 (tp) cc_final: 0.9310 (tp) REVERT: A 722 ASP cc_start: 0.8729 (t0) cc_final: 0.8352 (t70) REVERT: A 778 MET cc_start: 0.9206 (mmm) cc_final: 0.8940 (ttp) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.2806 time to fit residues: 133.4745 Evaluate side-chains 173 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.6980 chunk 137 optimal weight: 0.2980 chunk 76 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 142 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 165 optimal weight: 30.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 HIS B 159 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 HIS B 391 HIS ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 ASN A 53 HIS ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 HIS A 391 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 14399 Z= 0.364 Angle : 0.683 7.285 19521 Z= 0.354 Chirality : 0.045 0.236 2186 Planarity : 0.005 0.053 2478 Dihedral : 6.244 68.918 2076 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.43 % Allowed : 9.05 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.19), residues: 1818 helix: -0.89 (0.19), residues: 633 sheet: -2.03 (0.28), residues: 320 loop : -1.71 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 107 HIS 0.006 0.001 HIS D 61 PHE 0.029 0.002 PHE D 31 TYR 0.018 0.002 TYR B 209 ARG 0.009 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8473 (tmm) cc_final: 0.7931 (tmm) REVERT: B 40 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9369 (mm) REVERT: B 67 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8049 (mm-40) REVERT: B 222 ASN cc_start: 0.9026 (p0) cc_final: 0.8687 (p0) REVERT: B 429 MET cc_start: 0.8338 (mpt) cc_final: 0.8054 (mpp) REVERT: B 657 MET cc_start: 0.7161 (ppp) cc_final: 0.6383 (ppp) REVERT: B 722 ASP cc_start: 0.8573 (t0) cc_final: 0.8165 (t0) REVERT: C 45 LYS cc_start: 0.9038 (mttt) cc_final: 0.8765 (pttt) REVERT: C 64 ASP cc_start: 0.8680 (m-30) cc_final: 0.8407 (p0) REVERT: C 75 ASP cc_start: 0.8907 (t0) cc_final: 0.8688 (t0) REVERT: C 79 ASN cc_start: 0.9273 (m-40) cc_final: 0.8904 (t0) REVERT: C 83 LEU cc_start: 0.9096 (tp) cc_final: 0.8733 (tp) REVERT: C 112 TYR cc_start: 0.7954 (m-80) cc_final: 0.7653 (m-80) REVERT: D 75 ASP cc_start: 0.8816 (t0) cc_final: 0.8513 (t0) REVERT: D 83 LEU cc_start: 0.9178 (tp) cc_final: 0.7810 (tp) REVERT: D 109 ASP cc_start: 0.9479 (t0) cc_final: 0.9204 (t70) REVERT: A 31 MET cc_start: 0.8474 (tmm) cc_final: 0.7798 (tmm) REVERT: A 40 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9406 (mm) REVERT: A 67 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8091 (mm-40) REVERT: A 222 ASN cc_start: 0.8883 (p0) cc_final: 0.8402 (p0) REVERT: A 722 ASP cc_start: 0.8892 (t0) cc_final: 0.8459 (t70) REVERT: A 778 MET cc_start: 0.9335 (mmm) cc_final: 0.9062 (ttp) REVERT: A 818 PHE cc_start: 0.8341 (m-80) cc_final: 0.8082 (m-80) outliers start: 36 outliers final: 20 residues processed: 215 average time/residue: 0.2422 time to fit residues: 77.8728 Evaluate side-chains 176 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 56 optimal weight: 50.0000 chunk 132 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14399 Z= 0.368 Angle : 0.673 10.151 19521 Z= 0.342 Chirality : 0.044 0.219 2186 Planarity : 0.004 0.048 2478 Dihedral : 6.162 76.472 2076 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.97 % Allowed : 11.89 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.19), residues: 1818 helix: -0.17 (0.20), residues: 622 sheet: -1.92 (0.28), residues: 316 loop : -1.56 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 107 HIS 0.006 0.001 HIS C 61 PHE 0.025 0.002 PHE A 399 TYR 0.015 0.002 TYR B 209 ARG 0.004 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 163 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8380 (tmm) cc_final: 0.7941 (tmm) REVERT: B 40 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9350 (mm) REVERT: B 67 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8342 (mt0) REVERT: B 222 ASN cc_start: 0.8985 (p0) cc_final: 0.8606 (p0) REVERT: B 429 MET cc_start: 0.8338 (mpt) cc_final: 0.7996 (mpp) REVERT: B 657 MET cc_start: 0.7281 (ppp) cc_final: 0.6503 (ppp) REVERT: B 722 ASP cc_start: 0.8649 (t0) cc_final: 0.8183 (t0) REVERT: C 45 LYS cc_start: 0.9034 (mttt) cc_final: 0.8756 (pttp) REVERT: C 48 GLU cc_start: 0.7999 (pm20) cc_final: 0.7249 (pm20) REVERT: C 64 ASP cc_start: 0.8718 (m-30) cc_final: 0.8407 (p0) REVERT: C 79 ASN cc_start: 0.9328 (m-40) cc_final: 0.8866 (t0) REVERT: C 83 LEU cc_start: 0.9096 (tp) cc_final: 0.7824 (tp) REVERT: C 112 TYR cc_start: 0.7951 (m-80) cc_final: 0.7653 (m-80) REVERT: D 6 LEU cc_start: 0.8072 (mt) cc_final: 0.7572 (mt) REVERT: D 75 ASP cc_start: 0.8929 (t0) cc_final: 0.8622 (t0) REVERT: D 83 LEU cc_start: 0.8868 (tp) cc_final: 0.8509 (tp) REVERT: D 85 MET cc_start: 0.8673 (mpp) cc_final: 0.7710 (mpp) REVERT: D 109 ASP cc_start: 0.9497 (t0) cc_final: 0.9255 (t0) REVERT: A 31 MET cc_start: 0.8445 (tmm) cc_final: 0.7948 (tmm) REVERT: A 40 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9324 (mm) REVERT: A 67 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8308 (mt0) REVERT: A 222 ASN cc_start: 0.8998 (p0) cc_final: 0.8491 (p0) REVERT: A 469 MET cc_start: 0.8640 (mmp) cc_final: 0.8394 (mmp) REVERT: A 722 ASP cc_start: 0.8823 (t0) cc_final: 0.8395 (t70) REVERT: A 778 MET cc_start: 0.9332 (mmm) cc_final: 0.9089 (ttp) outliers start: 44 outliers final: 27 residues processed: 192 average time/residue: 0.2424 time to fit residues: 70.6897 Evaluate side-chains 176 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 85 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 40.0000 chunk 175 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN A 46 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14399 Z= 0.177 Angle : 0.563 9.611 19521 Z= 0.282 Chirality : 0.042 0.210 2186 Planarity : 0.003 0.045 2478 Dihedral : 5.749 74.828 2076 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.97 % Allowed : 13.38 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1818 helix: 0.49 (0.21), residues: 610 sheet: -1.59 (0.28), residues: 315 loop : -1.54 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 107 HIS 0.002 0.001 HIS C 61 PHE 0.019 0.001 PHE B 756 TYR 0.011 0.001 TYR A 797 ARG 0.004 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8262 (tmm) cc_final: 0.7941 (tmm) REVERT: B 67 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: B 429 MET cc_start: 0.8288 (mpt) cc_final: 0.7923 (mpp) REVERT: B 657 MET cc_start: 0.7359 (ppp) cc_final: 0.6619 (ppp) REVERT: B 722 ASP cc_start: 0.8596 (t0) cc_final: 0.8076 (t0) REVERT: C 45 LYS cc_start: 0.9032 (mttt) cc_final: 0.8776 (pttt) REVERT: C 48 GLU cc_start: 0.7884 (pm20) cc_final: 0.7214 (pm20) REVERT: C 64 ASP cc_start: 0.8716 (m-30) cc_final: 0.8412 (p0) REVERT: C 79 ASN cc_start: 0.9334 (m-40) cc_final: 0.8953 (t0) REVERT: C 83 LEU cc_start: 0.8912 (tp) cc_final: 0.8537 (tp) REVERT: C 85 MET cc_start: 0.8774 (mpp) cc_final: 0.8102 (mpp) REVERT: C 112 TYR cc_start: 0.7823 (m-80) cc_final: 0.7509 (m-80) REVERT: D 6 LEU cc_start: 0.8113 (mt) cc_final: 0.7550 (mt) REVERT: D 75 ASP cc_start: 0.8923 (t0) cc_final: 0.8718 (t0) REVERT: D 83 LEU cc_start: 0.8834 (tp) cc_final: 0.8228 (tp) REVERT: D 85 MET cc_start: 0.8647 (mpp) cc_final: 0.7784 (mpp) REVERT: D 109 ASP cc_start: 0.9427 (t0) cc_final: 0.9145 (t70) REVERT: A 31 MET cc_start: 0.8290 (tmm) cc_final: 0.7941 (tmm) REVERT: A 67 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8301 (mt0) REVERT: A 222 ASN cc_start: 0.8931 (p0) cc_final: 0.8383 (p0) REVERT: A 278 CYS cc_start: 0.8022 (m) cc_final: 0.7716 (m) REVERT: A 722 ASP cc_start: 0.8727 (t0) cc_final: 0.8302 (t70) REVERT: A 778 MET cc_start: 0.9329 (mmm) cc_final: 0.9072 (ttp) outliers start: 44 outliers final: 28 residues processed: 194 average time/residue: 0.2315 time to fit residues: 67.9188 Evaluate side-chains 179 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 157 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN A 350 HIS ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 14399 Z= 0.468 Angle : 0.736 8.879 19521 Z= 0.374 Chirality : 0.046 0.229 2186 Planarity : 0.004 0.045 2478 Dihedral : 6.281 78.876 2076 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 3.85 % Allowed : 14.26 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.19), residues: 1818 helix: 0.24 (0.20), residues: 609 sheet: -1.70 (0.28), residues: 306 loop : -1.53 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 107 HIS 0.006 0.002 HIS B 391 PHE 0.026 0.002 PHE B 399 TYR 0.013 0.002 TYR B 317 ARG 0.005 0.001 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 151 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8385 (tmm) cc_final: 0.7937 (tmm) REVERT: B 67 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: B 222 ASN cc_start: 0.8996 (p0) cc_final: 0.8502 (p0) REVERT: B 313 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.9043 (p) REVERT: B 329 LEU cc_start: 0.9647 (tp) cc_final: 0.9311 (tt) REVERT: B 429 MET cc_start: 0.8167 (mpt) cc_final: 0.7937 (mpp) REVERT: B 657 MET cc_start: 0.7246 (ppp) cc_final: 0.6530 (ppp) REVERT: B 722 ASP cc_start: 0.8708 (t0) cc_final: 0.8194 (t0) REVERT: C 45 LYS cc_start: 0.9017 (mttt) cc_final: 0.8713 (pttt) REVERT: C 48 GLU cc_start: 0.7882 (pm20) cc_final: 0.7226 (pm20) REVERT: C 64 ASP cc_start: 0.8714 (m-30) cc_final: 0.8364 (p0) REVERT: C 79 ASN cc_start: 0.9344 (m-40) cc_final: 0.9029 (t0) REVERT: C 112 TYR cc_start: 0.7844 (m-80) cc_final: 0.7540 (m-80) REVERT: D 6 LEU cc_start: 0.7961 (mt) cc_final: 0.7377 (mt) REVERT: D 75 ASP cc_start: 0.9077 (t0) cc_final: 0.8850 (t0) REVERT: D 83 LEU cc_start: 0.8896 (tp) cc_final: 0.8689 (tp) REVERT: D 109 ASP cc_start: 0.9412 (t0) cc_final: 0.9209 (t70) REVERT: A 31 MET cc_start: 0.8393 (tmm) cc_final: 0.7961 (tmm) REVERT: A 67 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8189 (mt0) REVERT: A 234 MET cc_start: 0.8851 (mtm) cc_final: 0.8522 (mtm) REVERT: A 313 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8979 (p) REVERT: A 436 LYS cc_start: 0.9458 (mmmt) cc_final: 0.9192 (mmtm) REVERT: A 722 ASP cc_start: 0.8643 (t0) cc_final: 0.8180 (t70) REVERT: A 728 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: A 778 MET cc_start: 0.9375 (mmm) cc_final: 0.9147 (ttp) REVERT: A 814 LEU cc_start: 0.8917 (mp) cc_final: 0.8672 (pp) outliers start: 57 outliers final: 44 residues processed: 193 average time/residue: 0.2490 time to fit residues: 71.9972 Evaluate side-chains 192 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 143 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 30.0000 chunk 158 optimal weight: 30.0000 chunk 34 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 GLN A 415 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14399 Z= 0.232 Angle : 0.604 12.893 19521 Z= 0.299 Chirality : 0.042 0.216 2186 Planarity : 0.003 0.043 2478 Dihedral : 5.849 79.087 2076 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.24 % Allowed : 16.01 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.20), residues: 1818 helix: 0.66 (0.21), residues: 610 sheet: -1.45 (0.29), residues: 306 loop : -1.43 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 107 HIS 0.003 0.001 HIS D 61 PHE 0.020 0.001 PHE B 756 TYR 0.008 0.001 TYR A 797 ARG 0.005 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 156 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8319 (tmm) cc_final: 0.8088 (tmm) REVERT: B 222 ASN cc_start: 0.8905 (p0) cc_final: 0.8358 (p0) REVERT: B 277 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.7706 (m-80) REVERT: B 313 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8860 (p) REVERT: B 429 MET cc_start: 0.8186 (mpt) cc_final: 0.7961 (mpp) REVERT: B 657 MET cc_start: 0.7141 (ppp) cc_final: 0.6362 (ppp) REVERT: B 722 ASP cc_start: 0.8656 (t0) cc_final: 0.8071 (t0) REVERT: C 20 LEU cc_start: 0.8896 (tp) cc_final: 0.8553 (tp) REVERT: C 45 LYS cc_start: 0.8970 (mttt) cc_final: 0.8693 (pttp) REVERT: C 48 GLU cc_start: 0.7932 (pm20) cc_final: 0.7358 (pm20) REVERT: C 64 ASP cc_start: 0.8705 (m-30) cc_final: 0.8389 (p0) REVERT: C 79 ASN cc_start: 0.9359 (m-40) cc_final: 0.9090 (t0) REVERT: C 85 MET cc_start: 0.8742 (mpp) cc_final: 0.8031 (mpp) REVERT: C 112 TYR cc_start: 0.7655 (m-80) cc_final: 0.7387 (m-80) REVERT: D 6 LEU cc_start: 0.7956 (mt) cc_final: 0.7382 (mt) REVERT: D 20 LEU cc_start: 0.8846 (tp) cc_final: 0.8538 (tp) REVERT: D 75 ASP cc_start: 0.8989 (t0) cc_final: 0.8771 (t0) REVERT: D 83 LEU cc_start: 0.8772 (tp) cc_final: 0.7827 (tp) REVERT: D 85 MET cc_start: 0.8643 (mpp) cc_final: 0.7751 (mpp) REVERT: D 109 ASP cc_start: 0.9386 (t0) cc_final: 0.9080 (t70) REVERT: A 31 MET cc_start: 0.8199 (tmm) cc_final: 0.7974 (tmm) REVERT: A 222 ASN cc_start: 0.9021 (p0) cc_final: 0.8429 (p0) REVERT: A 234 MET cc_start: 0.8780 (mtm) cc_final: 0.8533 (mtm) REVERT: A 313 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8826 (p) REVERT: A 722 ASP cc_start: 0.8576 (t0) cc_final: 0.7998 (p0) REVERT: A 778 MET cc_start: 0.9379 (mmm) cc_final: 0.9161 (ttp) outliers start: 48 outliers final: 36 residues processed: 189 average time/residue: 0.2320 time to fit residues: 66.9870 Evaluate side-chains 187 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 148 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 175 optimal weight: 30.0000 chunk 109 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 704 GLN C 120 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 14399 Z= 0.431 Angle : 0.724 13.647 19521 Z= 0.365 Chirality : 0.045 0.258 2186 Planarity : 0.004 0.042 2478 Dihedral : 6.256 79.296 2076 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 4.53 % Allowed : 14.80 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.19), residues: 1818 helix: 0.33 (0.20), residues: 609 sheet: -1.51 (0.28), residues: 304 loop : -1.50 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 500 HIS 0.005 0.002 HIS A 391 PHE 0.022 0.002 PHE B 399 TYR 0.012 0.001 TYR B 317 ARG 0.004 0.001 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 147 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 MET cc_start: 0.8345 (tmm) cc_final: 0.7983 (tmm) REVERT: B 222 ASN cc_start: 0.9109 (p0) cc_final: 0.8638 (p0) REVERT: B 257 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8885 (t80) REVERT: B 277 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: B 313 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.9001 (p) REVERT: B 329 LEU cc_start: 0.9652 (tp) cc_final: 0.9314 (tt) REVERT: B 429 MET cc_start: 0.8155 (mpt) cc_final: 0.7801 (mpp) REVERT: B 722 ASP cc_start: 0.8793 (t0) cc_final: 0.8269 (t0) REVERT: C 20 LEU cc_start: 0.8961 (tp) cc_final: 0.8657 (tp) REVERT: C 45 LYS cc_start: 0.8997 (mttt) cc_final: 0.8691 (pttt) REVERT: C 48 GLU cc_start: 0.7892 (pm20) cc_final: 0.7277 (pm20) REVERT: C 64 ASP cc_start: 0.8655 (m-30) cc_final: 0.8326 (p0) REVERT: C 79 ASN cc_start: 0.9361 (m-40) cc_final: 0.9074 (t0) REVERT: C 85 MET cc_start: 0.8745 (mpp) cc_final: 0.8097 (mpp) REVERT: D 6 LEU cc_start: 0.7877 (mt) cc_final: 0.7313 (mt) REVERT: D 75 ASP cc_start: 0.9024 (t0) cc_final: 0.8808 (t0) REVERT: D 83 LEU cc_start: 0.8779 (tp) cc_final: 0.7727 (tp) REVERT: D 85 MET cc_start: 0.8574 (mpp) cc_final: 0.7565 (mpp) REVERT: D 109 ASP cc_start: 0.9349 (t0) cc_final: 0.9100 (t70) REVERT: A 31 MET cc_start: 0.8260 (tmm) cc_final: 0.7964 (tmm) REVERT: A 197 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: A 234 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8636 (mtm) REVERT: A 257 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8717 (t80) REVERT: A 277 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: A 313 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8987 (p) REVERT: A 436 LYS cc_start: 0.9480 (mmmt) cc_final: 0.9196 (mmtm) REVERT: A 722 ASP cc_start: 0.8639 (t0) cc_final: 0.7951 (p0) REVERT: A 778 MET cc_start: 0.9399 (mmm) cc_final: 0.9193 (ttp) outliers start: 67 outliers final: 47 residues processed: 193 average time/residue: 0.2301 time to fit residues: 68.2333 Evaluate side-chains 200 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 145 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 496 ASP Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 0.0010 chunk 104 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN C 84 GLN C 120 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14399 Z= 0.155 Angle : 0.610 14.184 19521 Z= 0.295 Chirality : 0.042 0.187 2186 Planarity : 0.004 0.118 2478 Dihedral : 5.577 73.577 2076 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.18 % Allowed : 16.15 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1818 helix: 0.89 (0.21), residues: 619 sheet: -1.14 (0.30), residues: 300 loop : -1.37 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 107 HIS 0.004 0.001 HIS B 218 PHE 0.017 0.001 PHE B 756 TYR 0.015 0.001 TYR A 643 ARG 0.010 0.000 ARG C 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 162 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 ASN cc_start: 0.8874 (p0) cc_final: 0.8382 (p0) REVERT: B 257 PHE cc_start: 0.9223 (OUTLIER) cc_final: 0.8900 (t80) REVERT: B 313 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8709 (p) REVERT: B 429 MET cc_start: 0.8211 (mpt) cc_final: 0.7882 (mpp) REVERT: B 722 ASP cc_start: 0.8694 (t0) cc_final: 0.8110 (t0) REVERT: C 21 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6887 (ttm-80) REVERT: C 45 LYS cc_start: 0.8983 (mttt) cc_final: 0.8687 (pttp) REVERT: C 48 GLU cc_start: 0.7947 (pm20) cc_final: 0.7522 (pm20) REVERT: C 64 ASP cc_start: 0.8596 (m-30) cc_final: 0.8220 (p0) REVERT: C 79 ASN cc_start: 0.9360 (m-40) cc_final: 0.9114 (t0) REVERT: C 85 MET cc_start: 0.8757 (mpp) cc_final: 0.8112 (mpp) REVERT: D 6 LEU cc_start: 0.8026 (mt) cc_final: 0.7603 (mt) REVERT: D 59 SER cc_start: 0.9075 (m) cc_final: 0.8872 (p) REVERT: D 83 LEU cc_start: 0.8773 (tp) cc_final: 0.7903 (tp) REVERT: D 85 MET cc_start: 0.8607 (mpp) cc_final: 0.7803 (mpp) REVERT: D 109 ASP cc_start: 0.9354 (t0) cc_final: 0.9073 (t0) REVERT: D 113 ASP cc_start: 0.9320 (p0) cc_final: 0.9051 (p0) REVERT: A 222 ASN cc_start: 0.8826 (p0) cc_final: 0.8119 (p0) REVERT: A 257 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8699 (t80) REVERT: A 722 ASP cc_start: 0.8603 (t0) cc_final: 0.8044 (p0) REVERT: A 778 MET cc_start: 0.9299 (mmm) cc_final: 0.9096 (ttp) outliers start: 47 outliers final: 33 residues processed: 192 average time/residue: 0.2321 time to fit residues: 68.0865 Evaluate side-chains 192 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 155 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 50.0000 chunk 168 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14399 Z= 0.372 Angle : 0.725 14.124 19521 Z= 0.354 Chirality : 0.045 0.305 2186 Planarity : 0.004 0.091 2478 Dihedral : 5.945 78.083 2076 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.65 % Allowed : 16.08 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.89 (0.20), residues: 1818 helix: 0.74 (0.21), residues: 606 sheet: -1.24 (0.29), residues: 304 loop : -1.26 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 107 HIS 0.005 0.001 HIS B 30 PHE 0.019 0.002 PHE A 756 TYR 0.012 0.001 TYR C 114 ARG 0.011 0.001 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 149 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8155 (pt0) REVERT: B 222 ASN cc_start: 0.9002 (p0) cc_final: 0.8523 (p0) REVERT: B 257 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8922 (t80) REVERT: B 277 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.7937 (m-80) REVERT: B 313 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8849 (p) REVERT: B 329 LEU cc_start: 0.9615 (tp) cc_final: 0.9343 (tt) REVERT: B 429 MET cc_start: 0.8091 (mpt) cc_final: 0.7738 (mpp) REVERT: B 657 MET cc_start: 0.7113 (tmm) cc_final: 0.5867 (ppp) REVERT: B 722 ASP cc_start: 0.8743 (t0) cc_final: 0.8263 (p0) REVERT: C 21 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6827 (tpp80) REVERT: C 45 LYS cc_start: 0.8980 (mttt) cc_final: 0.8697 (pttp) REVERT: C 48 GLU cc_start: 0.7902 (pm20) cc_final: 0.7410 (pm20) REVERT: C 64 ASP cc_start: 0.8716 (m-30) cc_final: 0.8371 (p0) REVERT: C 79 ASN cc_start: 0.9372 (m-40) cc_final: 0.9144 (t0) REVERT: C 85 MET cc_start: 0.8765 (mpp) cc_final: 0.8221 (mpp) REVERT: D 6 LEU cc_start: 0.7928 (mt) cc_final: 0.7419 (mt) REVERT: D 83 LEU cc_start: 0.8817 (tp) cc_final: 0.7967 (tp) REVERT: D 85 MET cc_start: 0.8708 (mpp) cc_final: 0.7709 (mpp) REVERT: D 109 ASP cc_start: 0.9374 (t0) cc_final: 0.9110 (t70) REVERT: A 197 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8082 (pm20) REVERT: A 222 ASN cc_start: 0.9045 (p0) cc_final: 0.8355 (p0) REVERT: A 234 MET cc_start: 0.8802 (mtm) cc_final: 0.8546 (mtm) REVERT: A 257 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8762 (t80) REVERT: A 277 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: A 722 ASP cc_start: 0.8679 (t0) cc_final: 0.7955 (p0) REVERT: A 814 LEU cc_start: 0.8883 (mp) cc_final: 0.8484 (pp) outliers start: 54 outliers final: 41 residues processed: 186 average time/residue: 0.2205 time to fit residues: 63.5622 Evaluate side-chains 194 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 145 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 734 ASN Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 786 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 120 optimal weight: 0.3980 chunk 181 optimal weight: 5.9990 chunk 166 optimal weight: 50.0000 chunk 144 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14399 Z= 0.184 Angle : 0.677 15.743 19521 Z= 0.315 Chirality : 0.043 0.309 2186 Planarity : 0.003 0.070 2478 Dihedral : 5.637 74.042 2076 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.84 % Allowed : 17.57 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.77 (0.20), residues: 1818 helix: 0.86 (0.21), residues: 618 sheet: -1.06 (0.30), residues: 297 loop : -1.28 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 500 HIS 0.002 0.001 HIS C 61 PHE 0.022 0.001 PHE B 337 TYR 0.010 0.001 TYR C 114 ARG 0.009 0.000 ARG D 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3636 Ramachandran restraints generated. 1818 Oldfield, 0 Emsley, 1818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: B 222 ASN cc_start: 0.8836 (p0) cc_final: 0.8410 (p0) REVERT: B 257 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8883 (t80) REVERT: B 277 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: B 429 MET cc_start: 0.8162 (mpt) cc_final: 0.7856 (mpp) REVERT: B 657 MET cc_start: 0.7157 (tmm) cc_final: 0.6029 (ppp) REVERT: B 722 ASP cc_start: 0.8722 (t0) cc_final: 0.8286 (p0) REVERT: C 45 LYS cc_start: 0.8992 (mttt) cc_final: 0.8689 (pttp) REVERT: C 48 GLU cc_start: 0.7927 (pm20) cc_final: 0.7501 (pm20) REVERT: C 64 ASP cc_start: 0.8664 (m-30) cc_final: 0.8308 (p0) REVERT: C 75 ASP cc_start: 0.9063 (t0) cc_final: 0.8814 (t0) REVERT: C 79 ASN cc_start: 0.9352 (m-40) cc_final: 0.9090 (t0) REVERT: C 85 MET cc_start: 0.8729 (mpp) cc_final: 0.8101 (mpp) REVERT: D 6 LEU cc_start: 0.8031 (mt) cc_final: 0.7603 (mt) REVERT: D 83 LEU cc_start: 0.8873 (tp) cc_final: 0.8008 (tp) REVERT: D 85 MET cc_start: 0.8634 (mpp) cc_final: 0.7661 (mpp) REVERT: D 109 ASP cc_start: 0.9339 (t0) cc_final: 0.9069 (t0) REVERT: D 113 ASP cc_start: 0.9295 (p0) cc_final: 0.9038 (p0) REVERT: A 197 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: A 222 ASN cc_start: 0.8865 (p0) cc_final: 0.8133 (p0) REVERT: A 257 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8759 (t80) REVERT: A 657 MET cc_start: 0.6857 (ppp) cc_final: 0.6517 (ppp) REVERT: A 722 ASP cc_start: 0.8638 (t0) cc_final: 0.7927 (p0) outliers start: 42 outliers final: 35 residues processed: 187 average time/residue: 0.2256 time to fit residues: 65.8616 Evaluate side-chains 191 residues out of total 1574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 151 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 257 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 381 CYS Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 768 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.091442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.062074 restraints weight = 51832.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063775 restraints weight = 26445.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.064831 restraints weight = 17440.960| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14399 Z= 0.181 Angle : 0.665 15.495 19521 Z= 0.310 Chirality : 0.043 0.309 2186 Planarity : 0.003 0.050 2478 Dihedral : 5.480 72.312 2076 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.84 % Allowed : 17.70 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.68 (0.20), residues: 1818 helix: 0.91 (0.21), residues: 632 sheet: -0.99 (0.30), residues: 288 loop : -1.25 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 500 HIS 0.002 0.001 HIS B 30 PHE 0.020 0.001 PHE A 756 TYR 0.013 0.001 TYR C 114 ARG 0.010 0.000 ARG D 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2508.58 seconds wall clock time: 46 minutes 30.49 seconds (2790.49 seconds total)