Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 17:52:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oem_20030/07_2023/6oem_20030.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oem_20030/07_2023/6oem_20030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oem_20030/07_2023/6oem_20030.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oem_20030/07_2023/6oem_20030.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oem_20030/07_2023/6oem_20030.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oem_20030/07_2023/6oem_20030.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 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 Zn 2 6.06 5 P 204 5.49 5 Mg 2 5.21 5 S 106 5.16 5 C 11819 2.51 5 N 3476 2.21 5 O 4098 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 ARG 471": "NH1" <-> "NH2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A ARG 773": "NH1" <-> "NH2" Residue "A ARG 775": "NH1" <-> "NH2" Residue "A ARG 826": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A ARG 894": "NH1" <-> "NH2" Residue "A ARG 915": "NH1" <-> "NH2" Residue "A GLU 983": "OE1" <-> "OE2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ARG 409": "NH1" <-> "NH2" Residue "C ARG 773": "NH1" <-> "NH2" Residue "C ARG 826": "NH1" <-> "NH2" Residue "C ARG 838": "NH1" <-> "NH2" 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 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 19707 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4774 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 580} Chain breaks: 1 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 4, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 4843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4843 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 585} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 68 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2668 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2671 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1163 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} 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: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 947 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} 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: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2544 SG CYS A 727 88.110 24.912 57.634 1.00 91.74 S ATOM 2565 SG CYS A 730 88.645 22.480 57.782 1.00 90.71 S ATOM 7353 SG CYS C 727 61.828 106.636 58.091 1.00 82.68 S ATOM 7374 SG CYS C 730 61.375 108.925 56.753 1.00 82.68 S Time building chain proxies: 9.59, per 1000 atoms: 0.49 Number of scatterers: 19707 At special positions: 0 Unit cell: (150.87, 132.68, 157.29, 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 S 106 16.00 P 204 15.00 Mg 2 11.99 O 4098 8.00 N 3476 7.00 C 11819 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: 8.55 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " Number of angles added : 4 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3738 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 22 sheets defined 39.2% alpha, 19.2% beta 102 base pairs and 164 stacking pairs defined. Time for finding SS restraints: 6.55 Creating SS restraints... Processing helix chain 'A' and resid 400 through 423 removed outlier: 5.608A pdb=" N GLU A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 442 Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.501A pdb=" N ALA A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 478 through 493 Processing helix chain 'A' and resid 499 through 511 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 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.712A pdb=" N ASN A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 812 removed outlier: 3.804A pdb=" N ASN A 800 " --> pdb=" O CYS A 796 " (cutoff:3.500A) removed outlier: 3.719A 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: 3.647A pdb=" N ALA A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 868 removed outlier: 3.586A pdb=" N VAL A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 894 removed outlier: 4.075A 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: 3.556A pdb=" N LEU A 906 " --> pdb=" O CYS A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 923 removed outlier: 3.547A pdb=" N LEU A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 941 Processing helix chain 'A' and resid 942 through 950 removed outlier: 3.569A pdb=" N ILE A 946 " --> pdb=" O HIS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 975 Processing helix chain 'A' and resid 981 through 995 removed outlier: 4.274A pdb=" N GLU A 985 " --> pdb=" O CYS A 981 " (cutoff:3.500A) removed outlier: 3.542A 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 'A' and resid 1005 through 1007 No H-bonds generated for 'chain 'A' and resid 1005 through 1007' Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 400 through 423 removed outlier: 5.733A pdb=" N GLU C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) removed outlier: 5.609A 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 474 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 removed outlier: 3.503A pdb=" N LEU C 668 " --> pdb=" O ASP C 664 " (cutoff:3.500A) Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'C' and resid 733 through 740 removed outlier: 3.772A pdb=" N GLN C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) 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 813 removed outlier: 3.744A pdb=" N CYS C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) removed outlier: 3.550A 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 Processing helix chain 'C' and resid 859 through 868 Processing helix chain 'C' and resid 872 through 894 removed outlier: 3.965A pdb=" N HIS C 876 " --> pdb=" O SER C 872 " (cutoff:3.500A) 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 942 through 950 Processing helix chain 'C' and resid 963 through 974 removed outlier: 3.894A pdb=" N LEU C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 995 removed outlier: 4.158A 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 removed outlier: 3.583A pdb=" N ALA C1008 " --> pdb=" O ALA C1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1005 through 1008' Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'D' and resid 308 through 314 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 137 through 140 Processing helix chain 'H' and resid 141 through 155 Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 6.124A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.647A 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: 6.124A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ALA A 619 " --> pdb=" O MET A 602 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.403A 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: 9.880A pdb=" N PHE C 591 " --> pdb=" O PHE C 700 " (cutoff:3.500A) removed outlier: 10.573A pdb=" N PHE C 702 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N VAL C 593 " --> pdb=" O PHE C 702 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N GLY C 704 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 11.092A pdb=" N VAL C 595 " --> pdb=" O GLY C 704 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N GLY C 706 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLU C 597 " --> pdb=" O GLY C 706 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ALA C 619 " --> pdb=" O MET C 602 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 535 through 536 removed outlier: 6.666A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE C 631 " --> pdb=" O LYS C 639 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS C 639 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N HIS C 633 " --> pdb=" O ASN C 637 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN C 637 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.505A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 24 removed outlier: 3.819A pdb=" N LYS B 58 " --> pdb=" O HIS B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AA8, first strand: chain 'B' and resid 75 through 80 removed outlier: 3.595A pdb=" N CYS B 78 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 92 " --> pdb=" O CYS B 78 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 112 through 116 removed outlier: 7.031A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.630A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 141 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AB3, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.617A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 263 through 267 removed outlier: 3.713A pdb=" N THR B 264 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 5 Processing sheet with id=AB6, first strand: chain 'D' and resid 20 through 24 removed outlier: 3.789A pdb=" N LYS D 58 " --> pdb=" O HIS D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB8, first strand: chain 'D' and resid 75 through 80 Processing sheet with id=AB9, first strand: chain 'D' and resid 112 through 116 removed outlier: 6.784A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.048A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AC3, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.813A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 252 " --> pdb=" O LEU D 233 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 263 through 267 removed outlier: 3.780A pdb=" N THR D 264 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2028 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 253 hydrogen bonds 506 hydrogen bond angles 0 basepair planarities 102 basepair parallelities 164 stacking parallelities Total time for adding SS restraints: 10.23 Time building geometry restraints manager: 9.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5238 1.34 - 1.45: 4567 1.45 - 1.57: 10187 1.57 - 1.69: 406 1.69 - 1.81: 160 Bond restraints: 20558 Sorted by residual: bond pdb=" N GLU A 983 " pdb=" CA GLU A 983 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.15e+00 bond pdb=" N HIS C 609 " pdb=" CA HIS C 609 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.18e-02 7.18e+03 6.11e+00 bond pdb=" N ARG C 972 " pdb=" CA ARG C 972 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.33e-02 5.65e+03 5.97e+00 bond pdb=" N GLU C 983 " pdb=" CA GLU C 983 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.84e+00 bond pdb=" N GLU A 607 " pdb=" CA GLU A 607 " ideal model delta sigma weight residual 1.463 1.488 -0.025 1.24e-02 6.50e+03 4.08e+00 ... (remaining 20553 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.47: 1811 106.47 - 113.35: 10855 113.35 - 120.22: 7673 120.22 - 127.09: 7738 127.09 - 133.96: 631 Bond angle restraints: 28708 Sorted by residual: angle pdb=" N VAL A 742 " pdb=" CA VAL A 742 " pdb=" C VAL A 742 " ideal model delta sigma weight residual 106.21 110.09 -3.88 1.07e+00 8.73e-01 1.32e+01 angle pdb=" CA GLU A 607 " pdb=" C GLU A 607 " pdb=" O GLU A 607 " ideal model delta sigma weight residual 122.38 118.44 3.94 1.49e+00 4.50e-01 6.98e+00 angle pdb=" C3' DT G 25 " pdb=" O3' DT G 25 " pdb=" P DG G 26 " ideal model delta sigma weight residual 120.20 124.09 -3.89 1.50e+00 4.44e-01 6.71e+00 angle pdb=" CA GLU A 983 " pdb=" C GLU A 983 " pdb=" O GLU A 983 " ideal model delta sigma weight residual 120.82 118.16 2.66 1.05e+00 9.07e-01 6.42e+00 angle pdb=" CA HIS C 609 " pdb=" C HIS C 609 " pdb=" O HIS C 609 " ideal model delta sigma weight residual 120.90 118.31 2.59 1.03e+00 9.43e-01 6.30e+00 ... (remaining 28703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 10708 35.92 - 71.84: 849 71.84 - 107.76: 8 107.76 - 143.68: 7 143.68 - 179.60: 5 Dihedral angle restraints: 11577 sinusoidal: 5782 harmonic: 5795 Sorted by residual: dihedral pdb=" C4' DT J 14 " pdb=" C3' DT J 14 " pdb=" O3' DT J 14 " pdb=" P DT J 15 " ideal model delta sinusoidal sigma weight residual 220.00 40.40 179.60 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT G 29 " pdb=" C3' DT G 29 " pdb=" O3' DT G 29 " pdb=" P DT G 30 " ideal model delta sinusoidal sigma weight residual 220.00 40.97 179.03 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA F 33 " pdb=" C3' DA F 33 " pdb=" O3' DA F 33 " pdb=" P DG F 34 " ideal model delta sinusoidal sigma weight residual 220.00 42.48 177.52 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 11574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2228 0.029 - 0.059: 655 0.059 - 0.088: 159 0.088 - 0.118: 131 0.118 - 0.147: 12 Chirality restraints: 3185 Sorted by residual: chirality pdb=" CA ILE C 631 " pdb=" N ILE C 631 " pdb=" C ILE C 631 " pdb=" CB ILE C 631 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE B 331 " pdb=" N ILE B 331 " pdb=" C ILE B 331 " pdb=" CB ILE B 331 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE D 331 " pdb=" N ILE D 331 " pdb=" C ILE D 331 " pdb=" CB ILE D 331 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 3182 not shown) Planarity restraints: 2980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT G 24 " -0.018 2.00e-02 2.50e+03 9.54e-03 2.27e+00 pdb=" N1 DT G 24 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DT G 24 " 0.000 2.00e-02 2.50e+03 pdb=" O2 DT G 24 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DT G 24 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT G 24 " -0.002 2.00e-02 2.50e+03 pdb=" O4 DT G 24 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DT G 24 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT G 24 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT G 24 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 870 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 871 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 871 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 871 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 520 " -0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO A 521 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.016 5.00e-02 4.00e+02 ... (remaining 2977 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 69 2.50 - 3.10: 13244 3.10 - 3.70: 31187 3.70 - 4.30: 43109 4.30 - 4.90: 67157 Nonbonded interactions: 154766 Sorted by model distance: nonbonded pdb=" OD2 ASP C 708 " pdb="MG MG C1101 " model vdw 1.897 2.170 nonbonded pdb=" OD1 ASP C 600 " pdb="MG MG C1101 " model vdw 1.901 2.170 nonbonded pdb=" OD2 ASP A 708 " pdb="MG MG A1101 " model vdw 1.901 2.170 nonbonded pdb=" OD1 ASP A 600 " pdb="MG MG A1101 " model vdw 1.906 2.170 nonbonded pdb=" OD1 ASP A 546 " pdb=" OG SER B 260 " model vdw 2.210 2.440 ... (remaining 154761 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 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 n \ ame CA or name C or name O or name CB )) or resid 905 through 955 or (resid 956 \ and (name N or name CA or name C or name O or name CB )) or resid 961 through 10 \ 08 or resid 1101 through 1102)) 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 956 or resid 961 through 1008 or resid 1101 through 11 \ 02)) } ncs_group { reference = chain 'B' 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: 1.450 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: 5.360 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 60.580 Find NCS groups from input model: 0.940 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.002 0.050 20558 Z= 0.134 Angle : 0.493 6.051 28708 Z= 0.290 Chirality : 0.036 0.147 3185 Planarity : 0.003 0.031 2980 Dihedral : 19.813 179.604 7839 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 2.19 % 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: -2.82 (0.16), residues: 1978 helix: -0.65 (0.17), residues: 736 sheet: -1.80 (0.25), residues: 349 loop : -2.98 (0.17), residues: 893 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 199 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 6 residues processed: 228 average time/residue: 0.3125 time to fit residues: 109.9426 Evaluate side-chains 117 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.935 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1766 time to fit residues: 4.4248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN A 480 GLN A 498 GLN A 581 GLN A 739 GLN A 744 HIS A 860 GLN A 991 HIS C 456 GLN C 463 GLN C 473 ASN C 495 GLN C 515 HIS C 636 GLN C 637 ASN C 739 GLN C 744 HIS C 852 ASN B 47 HIS B 89 HIS ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 222 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN D 89 HIS D 94 HIS D 101 ASN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.072 20558 Z= 0.481 Angle : 0.779 13.724 28708 Z= 0.413 Chirality : 0.046 0.274 3185 Planarity : 0.006 0.045 2980 Dihedral : 25.313 176.913 4209 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer Outliers : 2.92 % 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: -1.99 (0.18), residues: 1978 helix: 0.07 (0.18), residues: 756 sheet: -1.25 (0.29), residues: 323 loop : -2.62 (0.18), residues: 899 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 98 time to evaluate : 1.951 Fit side-chains revert: symmetry clash outliers start: 48 outliers final: 28 residues processed: 140 average time/residue: 0.2685 time to fit residues: 63.1797 Evaluate side-chains 112 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 1.868 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1726 time to fit residues: 11.6115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 211 optimal weight: 50.0000 chunk 174 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 156 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 750 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7999 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 20558 Z= 0.235 Angle : 0.601 9.986 28708 Z= 0.319 Chirality : 0.040 0.171 3185 Planarity : 0.004 0.050 2980 Dihedral : 25.309 175.752 4209 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 1.77 % 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: -1.38 (0.19), residues: 1978 helix: 0.65 (0.19), residues: 756 sheet: -1.00 (0.28), residues: 342 loop : -2.34 (0.20), residues: 880 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 97 time to evaluate : 1.982 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 8 residues processed: 118 average time/residue: 0.2799 time to fit residues: 55.9946 Evaluate side-chains 94 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 2.076 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1982 time to fit residues: 5.5369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 193 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 93 optimal weight: 0.0970 chunk 131 optimal weight: 0.6980 chunk 196 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 overall best weight: 2.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 860 GLN ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8010 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 20558 Z= 0.223 Angle : 0.587 10.778 28708 Z= 0.315 Chirality : 0.040 0.169 3185 Planarity : 0.004 0.046 2980 Dihedral : 25.304 174.735 4209 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer Outliers : 1.46 % 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: -1.07 (0.19), residues: 1978 helix: 0.86 (0.19), residues: 760 sheet: -0.54 (0.30), residues: 326 loop : -2.24 (0.20), residues: 892 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 114 average time/residue: 0.2909 time to fit residues: 54.6219 Evaluate side-chains 95 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 1.926 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1722 time to fit residues: 5.3009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 173 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 154 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 4.9990 chunk 186 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 20558 Z= 0.260 Angle : 0.617 13.727 28708 Z= 0.330 Chirality : 0.040 0.164 3185 Planarity : 0.004 0.046 2980 Dihedral : 25.411 174.523 4209 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 2.38 % 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: -0.95 (0.19), residues: 1978 helix: 0.92 (0.19), residues: 760 sheet: -0.54 (0.29), residues: 337 loop : -2.12 (0.20), residues: 881 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 86 time to evaluate : 1.903 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 12 residues processed: 119 average time/residue: 0.2763 time to fit residues: 55.3415 Evaluate side-chains 97 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 2.029 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1824 time to fit residues: 6.7715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 69 optimal weight: 0.9980 chunk 187 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 20558 Z= 0.161 Angle : 0.565 12.360 28708 Z= 0.300 Chirality : 0.039 0.232 3185 Planarity : 0.003 0.047 2980 Dihedral : 25.317 176.331 4209 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 0.91 % 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: -0.64 (0.19), residues: 1978 helix: 1.20 (0.19), residues: 758 sheet: -0.25 (0.30), residues: 320 loop : -1.99 (0.20), residues: 900 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 102 average time/residue: 0.2816 time to fit residues: 48.3194 Evaluate side-chains 92 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1903 time to fit residues: 5.4713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 200 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 126 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 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: 0.8064 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 20558 Z= 0.296 Angle : 0.644 12.981 28708 Z= 0.345 Chirality : 0.041 0.167 3185 Planarity : 0.004 0.048 2980 Dihedral : 25.493 175.006 4209 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer Outliers : 1.22 % 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: -0.88 (0.19), residues: 1978 helix: 0.99 (0.19), residues: 759 sheet: -0.46 (0.30), residues: 324 loop : -2.10 (0.20), residues: 895 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 2.102 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 100 average time/residue: 0.2679 time to fit residues: 46.0974 Evaluate side-chains 88 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 1.882 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1801 time to fit residues: 5.5617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 128 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 188 optimal weight: 0.2980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 20558 Z= 0.171 Angle : 0.587 12.677 28708 Z= 0.311 Chirality : 0.039 0.168 3185 Planarity : 0.003 0.049 2980 Dihedral : 25.434 177.753 4209 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 0.37 % 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: -0.63 (0.19), residues: 1978 helix: 1.24 (0.19), residues: 757 sheet: -0.42 (0.29), residues: 332 loop : -1.95 (0.21), residues: 889 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 2.349 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 88 average time/residue: 0.2684 time to fit residues: 40.9895 Evaluate side-chains 84 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 2.054 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1785 time to fit residues: 2.9785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 chunk 193 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 151 optimal weight: 0.0670 chunk 59 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 20558 Z= 0.214 Angle : 0.604 13.659 28708 Z= 0.319 Chirality : 0.039 0.167 3185 Planarity : 0.004 0.048 2980 Dihedral : 25.448 176.883 4209 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 0.43 % 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: -0.52 (0.19), residues: 1978 helix: 1.40 (0.19), residues: 745 sheet: -0.31 (0.29), residues: 328 loop : -1.93 (0.20), residues: 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 2.006 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.2718 time to fit residues: 41.9963 Evaluate side-chains 85 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 2.015 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1762 time to fit residues: 3.7799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 204 optimal weight: 10.0000 chunk 124 optimal weight: 0.1980 chunk 96 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 135 optimal weight: 0.0870 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 991 HIS ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 20558 Z= 0.156 Angle : 0.590 19.524 28708 Z= 0.307 Chirality : 0.039 0.168 3185 Planarity : 0.003 0.048 2980 Dihedral : 25.392 179.092 4209 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.18 % 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: -0.33 (0.20), residues: 1978 helix: 1.53 (0.19), residues: 747 sheet: -0.25 (0.29), residues: 342 loop : -1.80 (0.21), residues: 889 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 1.976 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 90 average time/residue: 0.2687 time to fit residues: 41.7267 Evaluate side-chains 83 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.932 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 181 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 25 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 71 optimal weight: 0.1980 chunk 175 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.064483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.049792 restraints weight = 123455.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.050665 restraints weight = 62898.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.051175 restraints weight = 40442.311| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 20558 Z= 0.176 Angle : 0.597 12.857 28708 Z= 0.311 Chirality : 0.039 0.168 3185 Planarity : 0.003 0.048 2980 Dihedral : 25.400 178.503 4209 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer Outliers : 0.18 % 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: -0.29 (0.20), residues: 1978 helix: 1.56 (0.19), residues: 748 sheet: -0.09 (0.30), residues: 322 loop : -1.81 (0.20), residues: 908 =============================================================================== Job complete usr+sys time: 2612.78 seconds wall clock time: 49 minutes 24.39 seconds (2964.39 seconds total)