Starting phenix.real_space_refine on Sat Feb 17 19:09:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oen_20031/02_2024/6oen_20031.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oen_20031/02_2024/6oen_20031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oen_20031/02_2024/6oen_20031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oen_20031/02_2024/6oen_20031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oen_20031/02_2024/6oen_20031.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oen_20031/02_2024/6oen_20031.pdb" } resolution = 4.3 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Zn 2 6.06 5 P 204 5.49 5 S 106 5.16 5 C 11787 2.51 5 N 3467 2.21 5 O 4082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A GLU 662": "OE1" <-> "OE2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 826": "NH1" <-> "NH2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A ARG 894": "NH1" <-> "NH2" Residue "A ARG 915": "NH1" <-> "NH2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C GLU 507": "OE1" <-> "OE2" Residue "C PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 597": "OE1" <-> "OE2" Residue "C GLU 617": "OE1" <-> "OE2" Residue "C GLU 649": "OE1" <-> "OE2" Residue "C GLU 709": "OE1" <-> "OE2" Residue "C ARG 773": "NH1" <-> "NH2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" Residue "C GLU 877": "OE1" <-> "OE2" Residue "C ARG 915": "NH1" <-> "NH2" Residue "C ARG 927": "NH1" <-> "NH2" Residue "C ARG 970": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19649 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4770 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4820 Classifications: {'peptide': 609} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 583} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2664 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 2663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2663 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1154 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 936 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 938 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1171 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "N" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 242 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 288 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 3, 'TRANS': 51} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2544 SG CYS A 727 97.270 46.943 96.475 1.00117.57 S ATOM 2565 SG CYS A 730 99.151 45.527 97.280 1.00124.23 S ATOM 7340 SG CYS C 727 36.280 108.692 97.953 1.00 91.24 S ATOM 7361 SG CYS C 730 34.348 110.329 99.354 1.00 95.05 S Time building chain proxies: 10.79, per 1000 atoms: 0.55 Number of scatterers: 19649 At special positions: 0 Unit cell: (133.75, 160.5, 155.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 1 19.99 S 106 16.00 P 204 15.00 O 4082 8.00 N 3467 7.00 C 11787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 9.15 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 937 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 727 " Number of angles added : 4 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3734 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 20 sheets defined 39.7% alpha, 21.1% beta 100 base pairs and 177 stacking pairs defined. Time for finding SS restraints: 7.75 Creating SS restraints... Processing helix chain 'A' and resid 400 through 408 Processing helix chain 'A' and resid 408 through 423 Processing helix chain 'A' and resid 426 through 442 Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.938A pdb=" N ALA A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 475 removed outlier: 3.648A pdb=" N CYS A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.707A pdb=" N LEU A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 683 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.606A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 812 removed outlier: 3.966A pdb=" N ASN A 800 " --> pdb=" O CYS A 796 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 803 " --> pdb=" O GLY A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 841 Processing helix chain 'A' and resid 850 through 858 removed outlier: 3.512A pdb=" N ALA A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 Processing helix chain 'A' and resid 874 through 894 removed outlier: 3.606A pdb=" N ALA A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Proline residue: A 891 - end of helix Processing helix chain 'A' and resid 902 through 907 removed outlier: 3.747A pdb=" N LEU A 906 " --> pdb=" O CYS A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 923 Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 942 through 951 removed outlier: 3.934A pdb=" N ILE A 946 " --> pdb=" O HIS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 975 removed outlier: 3.629A pdb=" N ASN A 975 " --> pdb=" O PHE A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 995 removed outlier: 4.203A pdb=" N GLU A 985 " --> pdb=" O CYS A 981 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1004 Processing helix chain 'C' and resid 400 through 423 removed outlier: 5.457A pdb=" N GLU C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 441 Processing helix chain 'C' and resid 444 through 457 Processing helix chain 'C' and resid 463 through 475 removed outlier: 3.852A pdb=" N CYS C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 509 Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 664 through 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 776 Processing helix chain 'C' and resid 792 through 814 removed outlier: 3.877A pdb=" N LYS C 806 " --> pdb=" O ALA C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 841 Processing helix chain 'C' and resid 850 through 858 removed outlier: 3.697A pdb=" N MET C 858 " --> pdb=" O ALA C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 868 Processing helix chain 'C' and resid 873 through 894 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 902 through 907 Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 943 through 950 Processing helix chain 'C' and resid 963 through 975 removed outlier: 3.558A pdb=" N ASN C 975 " --> pdb=" O PHE C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 995 removed outlier: 4.228A pdb=" N GLU C 985 " --> pdb=" O CYS C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1004 Processing helix chain 'C' and resid 1005 through 1008 Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.900A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.900A pdb=" N LEU D 14 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'N' and resid 100 through 117 Proline residue: N 111 - end of helix Processing helix chain 'N' and resid 123 through 136 Processing helix chain 'H' and resid 102 through 117 Proline residue: H 111 - end of helix Processing helix chain 'H' and resid 121 through 136 Processing helix chain 'H' and resid 141 through 155 removed outlier: 3.665A pdb=" N GLU H 145 " --> pdb=" O LYS H 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 5.695A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 519 removed outlier: 5.695A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 518 through 519 removed outlier: 10.352A pdb=" N PHE C 591 " --> pdb=" O PHE C 700 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N PHE C 702 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N VAL C 593 " --> pdb=" O PHE C 702 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N GLY C 704 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 10.913A pdb=" N VAL C 595 " --> pdb=" O GLY C 704 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLY C 706 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU C 597 " --> pdb=" O GLY C 706 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET C 602 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL C 620 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP C 604 " --> pdb=" O LYS C 618 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LYS C 618 " --> pdb=" O ASP C 604 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 518 through 519 removed outlier: 10.352A pdb=" N PHE C 591 " --> pdb=" O PHE C 700 " (cutoff:3.500A) removed outlier: 11.270A pdb=" N PHE C 702 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N VAL C 593 " --> pdb=" O PHE C 702 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N GLY C 704 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 10.913A pdb=" N VAL C 595 " --> pdb=" O GLY C 704 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N GLY C 706 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU C 597 " --> pdb=" O GLY C 706 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET C 602 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL C 620 " --> pdb=" O MET C 602 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASP C 604 " --> pdb=" O LYS C 618 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LYS C 618 " --> pdb=" O ASP C 604 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 5 Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 24 removed outlier: 4.765A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS B 58 " --> pdb=" O HIS B 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 61 through 62 removed outlier: 7.701A pdb=" N ILE B 61 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 75 through 80 Processing sheet with id=AA9, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.328A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 193 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 182 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 183 " --> pdb=" O LEU B 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.607A pdb=" N ARG B 212 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 215 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 263 through 267 removed outlier: 7.100A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 271 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 2 through 5 Processing sheet with id=AB5, first strand: chain 'D' and resid 20 through 24 removed outlier: 4.765A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS D 58 " --> pdb=" O HIS D 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.701A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 75 through 80 Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.329A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 193 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 182 " --> pdb=" O TYR D 195 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE D 183 " --> pdb=" O LEU D 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AC1, first strand: chain 'D' and resid 208 through 212 removed outlier: 3.607A pdb=" N ARG D 212 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR D 215 " --> pdb=" O ARG D 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 263 through 267 removed outlier: 7.100A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE D 271 " --> pdb=" O VAL D 290 " (cutoff:3.500A) 739 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 249 hydrogen bonds 498 hydrogen bond angles 0 basepair planarities 100 basepair parallelities 177 stacking parallelities Total time for adding SS restraints: 10.61 Time building geometry restraints manager: 9.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5325 1.34 - 1.46: 6095 1.46 - 1.58: 8514 1.58 - 1.71: 404 1.71 - 1.83: 160 Bond restraints: 20498 Sorted by residual: bond pdb=" N HIS A 942 " pdb=" CA HIS A 942 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.12e-02 7.97e+03 1.02e+01 bond pdb=" N CYS C 730 " pdb=" CA CYS C 730 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.72e+00 bond pdb=" N HIS C 942 " pdb=" CA HIS C 942 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.38e+00 bond pdb=" N LEU A 718 " pdb=" CA LEU A 718 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.79e+00 bond pdb=" N GLU A 983 " pdb=" CA GLU A 983 " ideal model delta sigma weight residual 1.459 1.490 -0.030 1.19e-02 7.06e+03 6.46e+00 ... (remaining 20493 not shown) Histogram of bond angle deviations from ideal: 96.68 - 104.15: 958 104.15 - 111.61: 9652 111.61 - 119.07: 7178 119.07 - 126.54: 10008 126.54 - 134.00: 829 Bond angle restraints: 28625 Sorted by residual: angle pdb=" C SER A 895 " pdb=" N SER A 896 " pdb=" CA SER A 896 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C MET A 568 " pdb=" N ASP A 569 " pdb=" CA ASP A 569 " ideal model delta sigma weight residual 122.54 114.97 7.57 1.65e+00 3.67e-01 2.10e+01 angle pdb=" C CYS A 907 " pdb=" N GLN A 908 " pdb=" CA GLN A 908 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.07e+01 angle pdb=" C GLN A 962 " pdb=" N SER A 963 " pdb=" CA SER A 963 " ideal model delta sigma weight residual 120.54 126.51 -5.97 1.35e+00 5.49e-01 1.96e+01 angle pdb=" N SER A 723 " pdb=" CA SER A 723 " pdb=" C SER A 723 " ideal model delta sigma weight residual 110.33 115.55 -5.22 1.29e+00 6.01e-01 1.64e+01 ... (remaining 28620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 10546 35.73 - 71.46: 1193 71.46 - 107.20: 14 107.20 - 142.93: 5 142.93 - 178.66: 6 Dihedral angle restraints: 11764 sinusoidal: 5975 harmonic: 5789 Sorted by residual: dihedral pdb=" CA ARG D 212 " pdb=" C ARG D 212 " pdb=" N ASN D 213 " pdb=" CA ASN D 213 " ideal model delta harmonic sigma weight residual 180.00 151.49 28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ARG B 212 " pdb=" C ARG B 212 " pdb=" N ASN B 213 " pdb=" CA ASN B 213 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA PHE A 557 " pdb=" C PHE A 557 " pdb=" N ARG A 558 " pdb=" CA ARG A 558 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 11761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2252 0.050 - 0.100: 699 0.100 - 0.151: 176 0.151 - 0.201: 47 0.201 - 0.251: 7 Chirality restraints: 3181 Sorted by residual: chirality pdb=" CB ILE B 331 " pdb=" CA ILE B 331 " pdb=" CG1 ILE B 331 " pdb=" CG2 ILE B 331 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE D 331 " pdb=" CA ILE D 331 " pdb=" CG1 ILE D 331 " pdb=" CG2 ILE D 331 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL A 724 " pdb=" CA VAL A 724 " pdb=" CG1 VAL A 724 " pdb=" CG2 VAL A 724 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 3178 not shown) Planarity restraints: 2970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 511 " -0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO C 512 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 512 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 512 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 511 " 0.044 5.00e-02 4.00e+02 6.71e-02 7.21e+00 pdb=" N PRO A 512 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 941 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.00e+00 pdb=" C ALA A 941 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA A 941 " -0.017 2.00e-02 2.50e+03 pdb=" N HIS A 942 " -0.015 2.00e-02 2.50e+03 ... (remaining 2967 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2400 2.75 - 3.28: 17795 3.28 - 3.82: 36874 3.82 - 4.36: 39239 4.36 - 4.90: 62007 Nonbonded interactions: 158315 Sorted by model distance: nonbonded pdb=" C2' DA F 33 " pdb=" O5' DG F 34 " model vdw 2.208 3.440 nonbonded pdb=" OD1 ASP A 536 " pdb=" NZ LYS A 555 " model vdw 2.282 2.520 nonbonded pdb=" O CYS A 902 " pdb=" OG SER A 905 " model vdw 2.309 2.440 nonbonded pdb=" O SER C 539 " pdb=" OG SER C 539 " model vdw 2.315 2.440 nonbonded pdb=" OD2 ASP A 569 " pdb=" OG SER A 996 " model vdw 2.318 2.440 ... (remaining 158310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 400 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB )) or resid 408 through 427 or (resid 428 through 429 \ and (name N or name CA or name C or name O or name CB )) or resid 430 through 45 \ 7 or (resid 458 and (name N or name CA or name C or name O or name CB )) or resi \ d 459 through 584 or (resid 585 and (name N or name CA or name C or name O or na \ me CB )) or resid 586 through 606 or (resid 607 through 609 and (name N or name \ CA or name C or name O or name CB )) or resid 610 through 847 or (resid 848 and \ (name N or name CA or name C or name O or name CB )) or resid 849 through 903 or \ (resid 904 and (name N or name CA or name C or name O or name CB )) or resid 90 \ 5 through 954 or resid 961 through 1008 or resid 1101)) selection = (chain 'C' and (resid 400 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB )) or resid 410 through 631 or (resid 632 and (name N \ or name CA or name C or name O or name CB )) or resid 633 through 638 or (resid \ 639 and (name N or name CA or name C or name O or name CB )) or resid 640 throug \ h 751 or (resid 752 and (name N or name CA or name C or name O or name CB )) or \ resid 753 through 757 or (resid 758 and (name N or name CA or name C or name O o \ r name CB )) or resid 759 through 810 or (resid 811 and (name N or name CA or na \ me C or name O or name CB )) or resid 812 through 819 or (resid 820 through 821 \ and (name N or name CA or name C or name O or name CB )) or resid 822 or (resid \ 823 and (name N or name CA or name C or name O or name CB )) or resid 824 throug \ h 834 or (resid 835 and (name N or name CA or name C or name O or name CB )) or \ resid 836 through 837 or (resid 838 through 839 and (name N or name CA or name C \ or name O or name CB )) or resid 840 through 860 or (resid 861 and (name N or n \ ame CA or name C or name O or name CB )) or resid 862 through 926 or (resid 927 \ through 928 and (name N or name CA or name C or name O or name CB )) or resid 92 \ 9 through 947 or (resid 948 and (name N or name CA or name C or name O or name C \ B )) or resid 949 through 954 or resid 961 through 1008 or resid 1101)) } ncs_group { reference = (chain 'B' and (resid 1 through 117 or (resid 118 and (name N or name CA or name \ C or name O or name CB )) or resid 119 through 351)) selection = (chain 'D' and (resid 1 through 338 or (resid 339 and (name N or name CA or name \ C or name O or name CB )) or resid 340 through 351)) } 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.870 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 67.340 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.090 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 0.071 20498 Z= 0.385 Angle : 0.951 9.767 28625 Z= 0.546 Chirality : 0.054 0.251 3181 Planarity : 0.007 0.071 2970 Dihedral : 23.636 178.659 8030 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.61 % Allowed : 10.03 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -3.86 (0.15), residues: 1976 helix: -2.30 (0.14), residues: 716 sheet: -2.27 (0.24), residues: 350 loop : -2.84 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 133 HIS 0.009 0.002 HIS C1006 PHE 0.019 0.002 PHE C 418 TYR 0.027 0.002 TYR A 998 ARG 0.008 0.001 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 228 time to evaluate : 2.105 Fit side-chains REVERT: A 402 ARG cc_start: 0.2699 (ttt90) cc_final: 0.2232 (mmm160) REVERT: A 507 GLU cc_start: 0.8763 (tp30) cc_final: 0.8309 (tp30) REVERT: A 578 MET cc_start: 0.9118 (ttp) cc_final: 0.8673 (tpp) REVERT: A 678 GLU cc_start: 0.9036 (pp20) cc_final: 0.8807 (pp20) REVERT: A 687 LEU cc_start: 0.9043 (tp) cc_final: 0.8798 (tp) REVERT: A 889 MET cc_start: 0.8556 (mtm) cc_final: 0.8140 (mtm) REVERT: A 993 LEU cc_start: 0.9116 (mm) cc_final: 0.8827 (mp) REVERT: A 1003 MET cc_start: 0.8609 (mmm) cc_final: 0.8403 (mmm) REVERT: C 412 LYS cc_start: 0.9452 (tttt) cc_final: 0.9212 (tmtt) REVERT: C 617 GLU cc_start: 0.8265 (tt0) cc_final: 0.7991 (tt0) REVERT: B 20 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8134 (t) REVERT: B 49 ASP cc_start: 0.6997 (m-30) cc_final: 0.6610 (m-30) REVERT: B 111 SER cc_start: 0.7578 (OUTLIER) cc_final: 0.7378 (t) REVERT: D 110 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7896 (mmm) outliers start: 59 outliers final: 8 residues processed: 272 average time/residue: 0.3320 time to fit residues: 135.4898 Evaluate side-chains 138 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 7.9990 chunk 162 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 64 optimal weight: 0.0980 chunk 101 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 498 GLN A 501 HIS A 525 ASN A 744 HIS A 753 ASN A 755 GLN ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 GLN A 990 HIS C 495 GLN C 498 GLN C 588 ASN C 636 GLN ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS B 282 GLN B 313 HIS D 222 HIS D 282 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20498 Z= 0.191 Angle : 0.606 8.521 28625 Z= 0.334 Chirality : 0.040 0.195 3181 Planarity : 0.004 0.051 2970 Dihedral : 25.805 179.769 4421 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.24 % Allowed : 4.46 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -2.36 (0.17), residues: 1976 helix: -0.42 (0.18), residues: 728 sheet: -1.78 (0.27), residues: 288 loop : -2.44 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 317 HIS 0.007 0.001 HIS B 313 PHE 0.021 0.001 PHE A 418 TYR 0.015 0.001 TYR A 998 ARG 0.008 0.000 ARG C 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 191 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.2266 (ttt90) cc_final: 0.1970 (mmm160) REVERT: A 507 GLU cc_start: 0.8253 (tp30) cc_final: 0.7928 (tp30) REVERT: A 578 MET cc_start: 0.9076 (ttp) cc_final: 0.8576 (tpp) REVERT: A 687 LEU cc_start: 0.9101 (tp) cc_final: 0.8764 (tp) REVERT: A 881 GLU cc_start: 0.8864 (pt0) cc_final: 0.8506 (pp20) REVERT: A 889 MET cc_start: 0.8744 (mtm) cc_final: 0.8380 (mtm) REVERT: A 999 LEU cc_start: 0.9546 (mp) cc_final: 0.9269 (mt) REVERT: C 412 LYS cc_start: 0.9377 (tttt) cc_final: 0.9123 (tmtt) REVERT: C 504 ARG cc_start: 0.8112 (mtm-85) cc_final: 0.7698 (mtm-85) REVERT: C 507 GLU cc_start: 0.8013 (pt0) cc_final: 0.7718 (pp20) REVERT: B 67 CYS cc_start: 0.8670 (t) cc_final: 0.7404 (p) REVERT: B 152 MET cc_start: 0.9012 (tpp) cc_final: 0.8672 (tpp) REVERT: D 110 MET cc_start: 0.8384 (tpp) cc_final: 0.8043 (tpp) REVERT: D 219 LEU cc_start: 0.8765 (tp) cc_final: 0.8239 (tp) outliers start: 4 outliers final: 3 residues processed: 195 average time/residue: 0.3042 time to fit residues: 92.9210 Evaluate side-chains 130 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 127 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 132 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 210 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 HIS C 852 ASN C 991 HIS B 33 GLN B 89 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS D 33 GLN D 94 HIS ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20498 Z= 0.376 Angle : 0.722 13.021 28625 Z= 0.398 Chirality : 0.043 0.157 3181 Planarity : 0.005 0.070 2970 Dihedral : 25.897 178.797 4421 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.24 % Allowed : 6.79 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -2.01 (0.18), residues: 1976 helix: -0.05 (0.18), residues: 731 sheet: -1.59 (0.27), residues: 306 loop : -2.31 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 36 HIS 0.010 0.002 HIS A 795 PHE 0.031 0.002 PHE C 641 TYR 0.024 0.002 TYR A 998 ARG 0.007 0.001 ARG C 880 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 402 ARG cc_start: 0.2717 (ttt90) cc_final: 0.2323 (mmm160) REVERT: A 578 MET cc_start: 0.8977 (ttp) cc_final: 0.8701 (tpp) REVERT: A 687 LEU cc_start: 0.9200 (tp) cc_final: 0.8672 (tp) REVERT: A 795 HIS cc_start: 0.8604 (m90) cc_final: 0.8356 (m90) REVERT: A 889 MET cc_start: 0.8839 (mtm) cc_final: 0.8457 (mtm) REVERT: C 412 LYS cc_start: 0.9400 (tttt) cc_final: 0.9107 (tmtt) REVERT: C 602 MET cc_start: 0.9251 (mpp) cc_final: 0.9039 (mpp) REVERT: B 5 MET cc_start: 0.7917 (tpp) cc_final: 0.7519 (mmm) REVERT: B 110 MET cc_start: 0.8059 (tpt) cc_final: 0.7855 (tpt) REVERT: D 110 MET cc_start: 0.8338 (tpp) cc_final: 0.8109 (mmm) outliers start: 4 outliers final: 0 residues processed: 146 average time/residue: 0.2888 time to fit residues: 68.9374 Evaluate side-chains 104 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 92 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 HIS ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS B 33 GLN B 222 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20498 Z= 0.242 Angle : 0.626 12.162 28625 Z= 0.345 Chirality : 0.041 0.168 3181 Planarity : 0.004 0.061 2970 Dihedral : 25.753 179.130 4421 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.06 % Allowed : 3.30 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -1.53 (0.18), residues: 1976 helix: 0.35 (0.19), residues: 738 sheet: -1.25 (0.30), residues: 281 loop : -2.08 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 317 HIS 0.006 0.001 HIS A 501 PHE 0.019 0.001 PHE C 641 TYR 0.017 0.001 TYR C 998 ARG 0.003 0.000 ARG C 875 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 CYS cc_start: 0.8905 (m) cc_final: 0.8253 (t) REVERT: A 481 TYR cc_start: 0.8357 (t80) cc_final: 0.8107 (t80) REVERT: A 578 MET cc_start: 0.9106 (ttp) cc_final: 0.8745 (tpp) REVERT: A 627 MET cc_start: 0.8838 (pmm) cc_final: 0.8606 (pmm) REVERT: A 687 LEU cc_start: 0.9195 (tp) cc_final: 0.8903 (tp) REVERT: A 795 HIS cc_start: 0.8505 (m90) cc_final: 0.8008 (m-70) REVERT: A 881 GLU cc_start: 0.8987 (pt0) cc_final: 0.8595 (pp20) REVERT: A 886 TYR cc_start: 0.8441 (t80) cc_final: 0.8239 (t80) REVERT: A 889 MET cc_start: 0.8787 (mtm) cc_final: 0.8448 (mtm) REVERT: C 412 LYS cc_start: 0.9414 (tttt) cc_final: 0.9130 (tmtt) REVERT: C 682 MET cc_start: 0.8828 (mtt) cc_final: 0.8561 (mtt) REVERT: B 5 MET cc_start: 0.8049 (tpp) cc_final: 0.7679 (tpt) REVERT: D 110 MET cc_start: 0.8388 (tpp) cc_final: 0.8141 (mmm) outliers start: 1 outliers final: 1 residues processed: 153 average time/residue: 0.2740 time to fit residues: 69.5897 Evaluate side-chains 114 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 176 optimal weight: 0.0010 chunk 142 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 HIS ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 753 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN B 33 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20498 Z= 0.215 Angle : 0.603 12.276 28625 Z= 0.332 Chirality : 0.040 0.167 3181 Planarity : 0.004 0.050 2970 Dihedral : 25.632 177.520 4421 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -1.29 (0.19), residues: 1976 helix: 0.49 (0.19), residues: 755 sheet: -1.01 (0.29), residues: 305 loop : -1.99 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 317 HIS 0.006 0.001 HIS A 795 PHE 0.019 0.001 PHE A 418 TYR 0.014 0.001 TYR A 998 ARG 0.005 0.000 ARG C 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 2.228 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: A 455 MET cc_start: 0.8923 (mmp) cc_final: 0.8627 (mmm) REVERT: A 467 CYS cc_start: 0.8933 (m) cc_final: 0.8266 (t) REVERT: A 481 TYR cc_start: 0.8375 (t80) cc_final: 0.8025 (t80) REVERT: A 578 MET cc_start: 0.9081 (ttp) cc_final: 0.8736 (tpp) REVERT: A 627 MET cc_start: 0.8882 (pmm) cc_final: 0.8605 (pmm) REVERT: A 687 LEU cc_start: 0.9155 (tp) cc_final: 0.8862 (tp) REVERT: A 795 HIS cc_start: 0.8464 (m90) cc_final: 0.8173 (m-70) REVERT: A 889 MET cc_start: 0.8757 (mtm) cc_final: 0.8520 (mtm) REVERT: A 999 LEU cc_start: 0.9380 (mp) cc_final: 0.9019 (mp) REVERT: C 412 LYS cc_start: 0.9382 (tttt) cc_final: 0.9056 (tmtt) REVERT: C 682 MET cc_start: 0.8803 (mtt) cc_final: 0.8499 (mtt) REVERT: B 5 MET cc_start: 0.8019 (tpp) cc_final: 0.7672 (tpt) REVERT: D 110 MET cc_start: 0.8431 (tpp) cc_final: 0.8118 (mmm) REVERT: D 339 MET cc_start: 0.7021 (mmt) cc_final: 0.6812 (mmt) outliers start: 1 outliers final: 1 residues processed: 150 average time/residue: 0.2943 time to fit residues: 73.1504 Evaluate side-chains 112 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20498 Z= 0.163 Angle : 0.583 12.406 28625 Z= 0.316 Chirality : 0.040 0.169 3181 Planarity : 0.004 0.047 2970 Dihedral : 25.460 177.767 4421 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.06 % Allowed : 1.77 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -1.01 (0.19), residues: 1976 helix: 0.76 (0.19), residues: 756 sheet: -0.79 (0.29), residues: 305 loop : -1.89 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 317 HIS 0.004 0.001 HIS A 501 PHE 0.021 0.001 PHE A 418 TYR 0.011 0.001 TYR C 998 ARG 0.004 0.000 ARG C 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8820 (mmp) cc_final: 0.8475 (mmp) REVERT: A 467 CYS cc_start: 0.8926 (m) cc_final: 0.8180 (t) REVERT: A 481 TYR cc_start: 0.8354 (t80) cc_final: 0.8040 (t80) REVERT: A 578 MET cc_start: 0.9117 (ttp) cc_final: 0.8690 (tpp) REVERT: A 627 MET cc_start: 0.8893 (pmm) cc_final: 0.8624 (pmm) REVERT: A 687 LEU cc_start: 0.9179 (tp) cc_final: 0.8910 (tp) REVERT: A 795 HIS cc_start: 0.8460 (m90) cc_final: 0.8220 (m-70) REVERT: A 889 MET cc_start: 0.8809 (mtm) cc_final: 0.8422 (mtm) REVERT: A 1003 MET cc_start: 0.8256 (tpp) cc_final: 0.7006 (tmm) REVERT: C 412 LYS cc_start: 0.9356 (tttt) cc_final: 0.8993 (tmtt) REVERT: C 602 MET cc_start: 0.9092 (mpp) cc_final: 0.8748 (mpp) REVERT: C 658 MET cc_start: 0.8785 (pmm) cc_final: 0.7665 (pmm) REVERT: B 5 MET cc_start: 0.7904 (tpp) cc_final: 0.7619 (tpt) REVERT: D 110 MET cc_start: 0.8438 (tpp) cc_final: 0.8156 (mmm) REVERT: D 302 MET cc_start: 0.8642 (ppp) cc_final: 0.8438 (ppp) REVERT: D 339 MET cc_start: 0.7104 (mmt) cc_final: 0.6853 (mmt) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.2582 time to fit residues: 71.0713 Evaluate side-chains 123 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 206 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS D 33 GLN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 20498 Z= 0.413 Angle : 0.745 11.596 28625 Z= 0.407 Chirality : 0.044 0.172 3181 Planarity : 0.005 0.053 2970 Dihedral : 25.733 177.653 4421 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -1.36 (0.18), residues: 1976 helix: 0.47 (0.19), residues: 756 sheet: -0.90 (0.28), residues: 306 loop : -2.12 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 317 HIS 0.011 0.002 HIS A 795 PHE 0.030 0.002 PHE C 557 TYR 0.030 0.002 TYR C 559 ARG 0.009 0.001 ARG C 880 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 MET cc_start: 0.9150 (ttp) cc_final: 0.8787 (tpp) REVERT: A 795 HIS cc_start: 0.8654 (m90) cc_final: 0.8181 (m-70) REVERT: A 889 MET cc_start: 0.8862 (mtm) cc_final: 0.8544 (mtm) REVERT: C 412 LYS cc_start: 0.9388 (tttt) cc_final: 0.9065 (tmtt) REVERT: C 602 MET cc_start: 0.9212 (mpp) cc_final: 0.8967 (mpp) REVERT: C 986 ASP cc_start: 0.8614 (t70) cc_final: 0.8366 (t0) REVERT: D 152 MET cc_start: 0.9207 (tpp) cc_final: 0.8854 (tpt) REVERT: D 302 MET cc_start: 0.8707 (ppp) cc_final: 0.8243 (ppp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2755 time to fit residues: 61.3349 Evaluate side-chains 104 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 0.0270 chunk 62 optimal weight: 0.0570 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 740 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20498 Z= 0.177 Angle : 0.610 11.257 28625 Z= 0.330 Chirality : 0.041 0.170 3181 Planarity : 0.004 0.051 2970 Dihedral : 25.591 177.343 4421 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -0.99 (0.19), residues: 1976 helix: 0.79 (0.19), residues: 757 sheet: -0.79 (0.29), residues: 305 loop : -1.89 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 317 HIS 0.004 0.001 HIS A 795 PHE 0.026 0.001 PHE C 557 TYR 0.018 0.001 TYR A 886 ARG 0.003 0.000 ARG D 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.8737 (mmp) cc_final: 0.8479 (mmm) REVERT: A 578 MET cc_start: 0.9136 (ttp) cc_final: 0.8843 (tpp) REVERT: A 627 MET cc_start: 0.8871 (pmm) cc_final: 0.8602 (pmm) REVERT: A 687 LEU cc_start: 0.9182 (tp) cc_final: 0.8937 (tp) REVERT: A 795 HIS cc_start: 0.8526 (m90) cc_final: 0.8217 (m-70) REVERT: A 889 MET cc_start: 0.8683 (mtm) cc_final: 0.8406 (mtm) REVERT: C 412 LYS cc_start: 0.9370 (tttt) cc_final: 0.9018 (tmtt) REVERT: C 602 MET cc_start: 0.9164 (mpp) cc_final: 0.8842 (mpp) REVERT: C 658 MET cc_start: 0.8763 (pmm) cc_final: 0.7866 (pmm) REVERT: C 883 MET cc_start: 0.8681 (mmp) cc_final: 0.8464 (mmp) REVERT: C 986 ASP cc_start: 0.8521 (t70) cc_final: 0.8319 (t0) REVERT: B 152 MET cc_start: 0.8738 (tpp) cc_final: 0.8258 (tpp) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2855 time to fit residues: 73.9256 Evaluate side-chains 114 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 150 optimal weight: 0.0030 chunk 58 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 overall best weight: 5.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 744 HIS C 753 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS D 33 GLN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 20498 Z= 0.372 Angle : 0.716 10.658 28625 Z= 0.391 Chirality : 0.043 0.172 3181 Planarity : 0.005 0.052 2970 Dihedral : 25.726 178.237 4421 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.18), residues: 1976 helix: 0.44 (0.19), residues: 767 sheet: -0.93 (0.28), residues: 308 loop : -2.06 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 317 HIS 0.010 0.001 HIS A 795 PHE 0.027 0.002 PHE C 557 TYR 0.023 0.002 TYR C 559 ARG 0.005 0.001 ARG A 826 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 MET cc_start: 0.9109 (ttp) cc_final: 0.8875 (tpp) REVERT: A 627 MET cc_start: 0.8750 (pmm) cc_final: 0.8548 (pmm) REVERT: A 795 HIS cc_start: 0.8698 (m90) cc_final: 0.8268 (m-70) REVERT: A 889 MET cc_start: 0.8874 (mtm) cc_final: 0.8534 (mtm) REVERT: A 999 LEU cc_start: 0.9458 (mp) cc_final: 0.9243 (mp) REVERT: C 412 LYS cc_start: 0.9387 (tttt) cc_final: 0.9063 (tmtt) REVERT: C 602 MET cc_start: 0.9200 (mpp) cc_final: 0.8984 (mpp) REVERT: C 658 MET cc_start: 0.8967 (pmm) cc_final: 0.8227 (pmm) REVERT: C 986 ASP cc_start: 0.8614 (t70) cc_final: 0.8382 (t0) REVERT: B 152 MET cc_start: 0.8868 (tpp) cc_final: 0.8363 (tpp) REVERT: D 110 MET cc_start: 0.8093 (tpt) cc_final: 0.7845 (tpp) REVERT: D 302 MET cc_start: 0.8761 (ppp) cc_final: 0.8528 (ppp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2745 time to fit residues: 60.7972 Evaluate side-chains 103 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20498 Z= 0.337 Angle : 0.696 10.757 28625 Z= 0.381 Chirality : 0.043 0.183 3181 Planarity : 0.005 0.048 2970 Dihedral : 25.823 177.168 4421 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -1.36 (0.18), residues: 1976 helix: 0.49 (0.19), residues: 742 sheet: -1.00 (0.30), residues: 286 loop : -2.05 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 317 HIS 0.011 0.001 HIS A 515 PHE 0.025 0.002 PHE C 557 TYR 0.024 0.002 TYR C 559 ARG 0.005 0.001 ARG C 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 578 MET cc_start: 0.9073 (ttp) cc_final: 0.8800 (tpp) REVERT: A 627 MET cc_start: 0.8796 (pmm) cc_final: 0.8554 (pmm) REVERT: A 658 MET cc_start: 0.8487 (pmm) cc_final: 0.7539 (pmm) REVERT: A 687 LEU cc_start: 0.9176 (tp) cc_final: 0.8844 (tp) REVERT: A 795 HIS cc_start: 0.8672 (m90) cc_final: 0.8279 (m-70) REVERT: A 883 MET cc_start: 0.8707 (ttt) cc_final: 0.8315 (ttp) REVERT: A 889 MET cc_start: 0.8839 (mtm) cc_final: 0.8539 (mtm) REVERT: A 999 LEU cc_start: 0.9412 (mp) cc_final: 0.9133 (mp) REVERT: C 412 LYS cc_start: 0.9384 (tttt) cc_final: 0.9061 (tmtt) REVERT: C 578 MET cc_start: 0.9246 (pmm) cc_final: 0.8892 (pmm) REVERT: C 602 MET cc_start: 0.9248 (mpp) cc_final: 0.8971 (mpp) REVERT: C 658 MET cc_start: 0.8891 (pmm) cc_final: 0.8222 (pmm) REVERT: C 682 MET cc_start: 0.8772 (mtt) cc_final: 0.8559 (mtt) REVERT: C 858 MET cc_start: 0.8726 (tpp) cc_final: 0.8441 (tpt) REVERT: C 986 ASP cc_start: 0.8548 (t70) cc_final: 0.8331 (t0) REVERT: B 110 MET cc_start: 0.7978 (tpt) cc_final: 0.7677 (tpt) REVERT: B 152 MET cc_start: 0.8869 (tpp) cc_final: 0.8348 (tpp) REVERT: D 110 MET cc_start: 0.8017 (tpt) cc_final: 0.7816 (tpp) REVERT: D 302 MET cc_start: 0.8747 (ppp) cc_final: 0.8542 (ppp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.2755 time to fit residues: 61.5679 Evaluate side-chains 104 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** D 282 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 = 0.3487 r_free = 0.3487 target = 0.065926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.047002 restraints weight = 119862.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.048120 restraints weight = 66978.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048850 restraints weight = 45224.622| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20498 Z= 0.195 Angle : 0.624 10.748 28625 Z= 0.338 Chirality : 0.041 0.177 3181 Planarity : 0.004 0.050 2970 Dihedral : 25.618 179.231 4421 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % 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: -1.05 (0.19), residues: 1976 helix: 0.70 (0.19), residues: 757 sheet: -0.84 (0.28), residues: 311 loop : -1.88 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 307 HIS 0.005 0.001 HIS A 795 PHE 0.024 0.001 PHE C 557 TYR 0.015 0.001 TYR C 559 ARG 0.004 0.000 ARG A 970 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3174.38 seconds wall clock time: 59 minutes 31.84 seconds (3571.84 seconds total)