Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 20:28:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftx_4318/04_2023/6ftx_4318_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftx_4318/04_2023/6ftx_4318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftx_4318/04_2023/6ftx_4318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftx_4318/04_2023/6ftx_4318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftx_4318/04_2023/6ftx_4318_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ftx_4318/04_2023/6ftx_4318_neut_updated.pdb" } resolution = 4.5 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= 0.000 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 P 320 5.49 5 S 41 5.16 5 Be 1 3.05 5 C 12267 2.51 5 N 3844 2.21 5 O 4573 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "N GLU 24": "OE1" <-> "OE2" Residue "W ARG 807": "NH1" <-> "NH2" Residue "W PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 1202": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 21049 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 866 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "F" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 686 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 90} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3238 Classifications: {'DNA': 159} Link IDs: {'rna3p': 158} Chain: "J" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3298 Classifications: {'DNA': 160} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 159} Chain: "N" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "O" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "W" Number of atoms: 7220 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 880, 7204 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'peptide': 878, 'undetermined': 2} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 848, None: 2} Not linked: pdbres="ASN W1268 " pdbres="BEF W1301 " Not linked: pdbres="BEF W1301 " pdbres="ADP W1302 " Chain breaks: 5 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 880, 7204 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'peptide': 878, 'undetermined': 2} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 848, None: 2} Not linked: pdbres="ASN W1268 " pdbres="BEF W1301 " Not linked: pdbres="BEF W1301 " pdbres="ADP W1302 " Chain breaks: 5 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 7326 Time building chain proxies: 14.60, per 1000 atoms: 0.69 Number of scatterers: 21049 At special positions: 0 Unit cell: (152.6, 147, 173.6, 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) S 41 16.00 P 320 15.00 F 3 9.00 O 4573 8.00 N 3844 7.00 C 12267 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS W 207 " - pdb=" SG CYS W 246 " distance=2.82 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.54 Conformation dependent library (CDL) restraints added in 3.1 seconds 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3402 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 10 sheets defined 47.3% alpha, 4.4% beta 84 base pairs and 219 stacking pairs defined. Time for finding SS restraints: 7.47 Creating SS restraints... Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.580A pdb=" N GLN A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.541A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.627A pdb=" N ALA B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 75 removed outlier: 3.781A pdb=" N TYR B 51 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU B 52 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR B 54 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 63 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 66 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 70 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR B 71 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 18 through 21 No H-bonds generated for 'chain 'C' and resid 18 through 21' Processing helix chain 'C' and resid 27 through 36 removed outlier: 4.092A pdb=" N HIS C 31 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 33 " --> pdb=" O ARG C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.961A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 63 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 removed outlier: 3.561A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 55 through 78 removed outlier: 3.602A pdb=" N GLU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 3.587A pdb=" N ARG D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.752A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 56 Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.535A pdb=" N VAL E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG E 72 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.721A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 131 removed outlier: 3.730A pdb=" N ALA E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 41 removed outlier: 3.789A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 75 removed outlier: 3.877A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 34 Processing helix chain 'G' and resid 47 through 72 removed outlier: 4.232A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.544A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 99 removed outlier: 4.680A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG G 99 " --> pdb=" O LYS G 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 45 removed outlier: 3.643A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 removed outlier: 3.661A pdb=" N ILE H 70 " --> pdb=" O VAL H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 98 removed outlier: 3.524A pdb=" N ALA H 94 " --> pdb=" O GLU H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.736A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 30 removed outlier: 3.546A pdb=" N LYS N 29 " --> pdb=" O ASN N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'O' and resid 23 through 34 Processing helix chain 'O' and resid 57 through 59 No H-bonds generated for 'chain 'O' and resid 57 through 59' Processing helix chain 'W' and resid 204 through 210 Processing helix chain 'W' and resid 240 through 256 removed outlier: 3.506A pdb=" N ASN W 244 " --> pdb=" O LYS W 240 " (cutoff:3.500A) Processing helix chain 'W' and resid 265 through 284 removed outlier: 4.161A pdb=" N ARG W 274 " --> pdb=" O MET W 270 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU W 283 " --> pdb=" O ASP W 279 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE W 284 " --> pdb=" O GLU W 280 " (cutoff:3.500A) Processing helix chain 'W' and resid 332 through 343 removed outlier: 3.834A pdb=" N GLU W 342 " --> pdb=" O PHE W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 384 through 387 No H-bonds generated for 'chain 'W' and resid 384 through 387' Processing helix chain 'W' and resid 407 through 417 removed outlier: 3.514A pdb=" N THR W 411 " --> pdb=" O LYS W 407 " (cutoff:3.500A) Processing helix chain 'W' and resid 437 through 445 Processing helix chain 'W' and resid 461 through 470 removed outlier: 3.650A pdb=" N ARG W 467 " --> pdb=" O ARG W 463 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR W 469 " --> pdb=" O THR W 465 " (cutoff:3.500A) Processing helix chain 'W' and resid 492 through 497 removed outlier: 3.814A pdb=" N LEU W 496 " --> pdb=" O TYR W 492 " (cutoff:3.500A) Processing helix chain 'W' and resid 499 through 504 Processing helix chain 'W' and resid 549 through 559 Processing helix chain 'W' and resid 579 through 593 removed outlier: 3.766A pdb=" N ARG W 588 " --> pdb=" O HIS W 584 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN W 591 " --> pdb=" O HIS W 587 " (cutoff:3.500A) Proline residue: W 592 - end of helix Processing helix chain 'W' and resid 620 through 630 removed outlier: 3.913A pdb=" N GLU W 624 " --> pdb=" O ASP W 620 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE W 629 " --> pdb=" O TYR W 625 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU W 630 " --> pdb=" O TYR W 626 " (cutoff:3.500A) Processing helix chain 'W' and resid 640 through 652 removed outlier: 4.161A pdb=" N GLY W 644 " --> pdb=" O GLY W 640 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N HIS W 645 " --> pdb=" O ALA W 641 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE W 646 " --> pdb=" O LYS W 642 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU W 648 " --> pdb=" O GLY W 644 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU W 649 " --> pdb=" O HIS W 645 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE W 651 " --> pdb=" O SER W 647 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET W 652 " --> pdb=" O LEU W 648 " (cutoff:3.500A) Processing helix chain 'W' and resid 669 through 672 No H-bonds generated for 'chain 'W' and resid 669 through 672' Processing helix chain 'W' and resid 684 through 692 Processing helix chain 'W' and resid 695 through 708 Processing helix chain 'W' and resid 721 through 731 removed outlier: 3.712A pdb=" N ASP W 725 " --> pdb=" O VAL W 721 " (cutoff:3.500A) Processing helix chain 'W' and resid 747 through 758 removed outlier: 3.679A pdb=" N SER W 753 " --> pdb=" O GLN W 749 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE W 754 " --> pdb=" O ARG W 750 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP W 755 " --> pdb=" O ARG W 751 " (cutoff:3.500A) Processing helix chain 'W' and resid 797 through 803 Processing helix chain 'W' and resid 826 through 837 Processing helix chain 'W' and resid 1011 through 1024 removed outlier: 3.835A pdb=" N LYS W1019 " --> pdb=" O ARG W1015 " (cutoff:3.500A) Processing helix chain 'W' and resid 1028 through 1036 removed outlier: 3.824A pdb=" N LEU W1031 " --> pdb=" O LYS W1028 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASP W1032 " --> pdb=" O GLU W1029 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU W1034 " --> pdb=" O LEU W1031 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA W1036 " --> pdb=" O GLU W1033 " (cutoff:3.500A) Processing helix chain 'W' and resid 1045 through 1090 removed outlier: 3.537A pdb=" N GLY W1049 " --> pdb=" O PHE W1045 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR W1051 " --> pdb=" O LYS W1047 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET W1056 " --> pdb=" O TYR W1052 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP W1061 " --> pdb=" O GLU W1057 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS W1062 " --> pdb=" O ALA W1058 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL W1063 " --> pdb=" O ALA W1059 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS W1076 " --> pdb=" O GLU W1072 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA W1083 " --> pdb=" O LYS W1079 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS W1087 " --> pdb=" O ALA W1083 " (cutoff:3.500A) Processing helix chain 'W' and resid 1103 through 1111 Processing helix chain 'W' and resid 1129 through 1147 removed outlier: 3.512A pdb=" N LEU W1133 " --> pdb=" O ALA W1129 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU W1137 " --> pdb=" O LEU W1133 " (cutoff:3.500A) Processing helix chain 'W' and resid 1154 through 1156 No H-bonds generated for 'chain 'W' and resid 1154 through 1156' Processing helix chain 'W' and resid 1176 through 1189 removed outlier: 3.541A pdb=" N ILE W1184 " --> pdb=" O GLU W1180 " (cutoff:3.500A) Processing helix chain 'W' and resid 1195 through 1199 Processing helix chain 'W' and resid 1249 through 1264 removed outlier: 3.761A pdb=" N ASP W1257 " --> pdb=" O GLY W1253 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR W1258 " --> pdb=" O ARG W1254 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG W1264 " --> pdb=" O LEU W1260 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.583A pdb=" N LEU N 15 " --> pdb=" O ILE N 3 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL N 5 " --> pdb=" O ILE N 13 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE N 13 " --> pdb=" O VAL N 5 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 42 through 44 Processing sheet with id= C, first strand: chain 'O' and resid 12 through 16 Processing sheet with id= D, first strand: chain 'W' and resid 184 through 187 removed outlier: 3.789A pdb=" N ASN W 184 " --> pdb=" O LEU W 214 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE W 213 " --> pdb=" O GLU W 228 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'W' and resid 292 through 297 removed outlier: 4.005A pdb=" N ASP W 292 " --> pdb=" O LEU W 308 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'W' and resid 397 through 399 removed outlier: 3.952A pdb=" N LEU W 539 " --> pdb=" O GLY W 397 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'W' and resid 488 through 490 Processing sheet with id= H, first strand: chain 'W' and resid 815 through 818 removed outlier: 4.150A pdb=" N GLN W 739 " --> pdb=" O VAL W 766 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU W 768 " --> pdb=" O GLN W 739 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'W' and resid 179 through 182 removed outlier: 7.269A pdb=" N LYS W 216 " --> pdb=" O ASP W 180 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'W' and resid 287 through 290 removed outlier: 6.867A pdb=" N LYS W 310 " --> pdb=" O GLU W 288 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 196 hydrogen bonds 380 hydrogen bond angles 0 basepair planarities 84 basepair parallelities 219 stacking parallelities Total time for adding SS restraints: 11.37 Time building geometry restraints manager: 12.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.26: 2383 1.26 - 1.43: 7265 1.43 - 1.59: 11902 1.59 - 1.76: 452 1.76 - 1.92: 75 Bond restraints: 22077 Sorted by residual: bond pdb=" BE BEF W1301 " pdb=" F2 BEF W1301 " ideal model delta sigma weight residual 1.476 1.823 -0.347 2.00e-02 2.50e+03 3.01e+02 bond pdb=" BE BEF W1301 " pdb=" F3 BEF W1301 " ideal model delta sigma weight residual 1.476 1.783 -0.307 2.00e-02 2.50e+03 2.35e+02 bond pdb=" BE BEF W1301 " pdb=" F1 BEF W1301 " ideal model delta sigma weight residual 1.476 1.744 -0.268 2.00e-02 2.50e+03 1.79e+02 bond pdb=" C ILE C 102 " pdb=" O ILE C 102 " ideal model delta sigma weight residual 1.236 1.356 -0.120 1.00e-02 1.00e+04 1.45e+02 bond pdb=" C THR D 87 " pdb=" O THR D 87 " ideal model delta sigma weight residual 1.234 1.097 0.137 1.16e-02 7.43e+03 1.39e+02 ... (remaining 22072 not shown) Histogram of bond angle deviations from ideal: 88.29 - 98.01: 22 98.01 - 107.74: 4041 107.74 - 117.46: 13775 117.46 - 127.19: 12457 127.19 - 136.91: 873 Bond angle restraints: 31168 Sorted by residual: angle pdb=" CA ALA G 47 " pdb=" C ALA G 47 " pdb=" N PRO G 48 " ideal model delta sigma weight residual 120.52 109.66 10.86 8.30e-01 1.45e+00 1.71e+02 angle pdb=" N TYR C 39 " pdb=" CA TYR C 39 " pdb=" C TYR C 39 " ideal model delta sigma weight residual 110.97 121.99 -11.02 1.09e+00 8.42e-01 1.02e+02 angle pdb=" CB GLU O 64 " pdb=" CG GLU O 64 " pdb=" CD GLU O 64 " ideal model delta sigma weight residual 112.60 128.89 -16.29 1.70e+00 3.46e-01 9.18e+01 angle pdb=" NE ARG B 40 " pdb=" CZ ARG B 40 " pdb=" NH1 ARG B 40 " ideal model delta sigma weight residual 121.50 112.46 9.04 1.00e+00 1.00e+00 8.18e+01 angle pdb=" CA ARG G 17 " pdb=" C ARG G 17 " pdb=" O ARG G 17 " ideal model delta sigma weight residual 120.82 111.56 9.26 1.05e+00 9.07e-01 7.78e+01 ... (remaining 31163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 10556 35.12 - 70.24: 1629 70.24 - 105.36: 67 105.36 - 140.49: 4 140.49 - 175.61: 1 Dihedral angle restraints: 12257 sinusoidal: 6996 harmonic: 5261 Sorted by residual: dihedral pdb=" CD ARG D 30 " pdb=" NE ARG D 30 " pdb=" CZ ARG D 30 " pdb=" NH1 ARG D 30 " ideal model delta sinusoidal sigma weight residual 0.00 87.52 -87.52 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CD ARG G 77 " pdb=" NE ARG G 77 " pdb=" CZ ARG G 77 " pdb=" NH1 ARG G 77 " ideal model delta sinusoidal sigma weight residual 0.00 87.05 -87.05 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" C ASN D 81 " pdb=" N ASN D 81 " pdb=" CA ASN D 81 " pdb=" CB ASN D 81 " ideal model delta harmonic sigma weight residual -122.60 -144.97 22.37 0 2.50e+00 1.60e-01 8.01e+01 ... (remaining 12254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 2942 0.157 - 0.314: 505 0.314 - 0.471: 50 0.471 - 0.628: 9 0.628 - 0.784: 2 Chirality restraints: 3508 Sorted by residual: chirality pdb=" CA ASN D 81 " pdb=" N ASN D 81 " pdb=" C ASN D 81 " pdb=" CB ASN D 81 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" C3' DG I -52 " pdb=" C4' DG I -52 " pdb=" O3' DG I -52 " pdb=" C2' DG I -52 " both_signs ideal model delta sigma weight residual False -2.66 -1.96 -0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA LEU O 71 " pdb=" N LEU O 71 " pdb=" C LEU O 71 " pdb=" CB LEU O 71 " both_signs ideal model delta sigma weight residual False 2.51 3.11 -0.60 2.00e-01 2.50e+01 8.92e+00 ... (remaining 3505 not shown) Planarity restraints: 2863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 30 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG D 30 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG D 30 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 30 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG D 30 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 77 " 1.098 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG G 77 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 77 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 77 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG G 77 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -19 " -0.149 2.00e-02 2.50e+03 6.23e-02 1.16e+02 pdb=" N9 DG J -19 " 0.038 2.00e-02 2.50e+03 pdb=" C8 DG J -19 " 0.027 2.00e-02 2.50e+03 pdb=" N7 DG J -19 " 0.034 2.00e-02 2.50e+03 pdb=" C5 DG J -19 " 0.027 2.00e-02 2.50e+03 pdb=" C6 DG J -19 " -0.050 2.00e-02 2.50e+03 pdb=" O6 DG J -19 " -0.046 2.00e-02 2.50e+03 pdb=" N1 DG J -19 " -0.049 2.00e-02 2.50e+03 pdb=" C2 DG J -19 " 0.049 2.00e-02 2.50e+03 pdb=" N2 DG J -19 " -0.024 2.00e-02 2.50e+03 pdb=" N3 DG J -19 " 0.073 2.00e-02 2.50e+03 pdb=" C4 DG J -19 " 0.070 2.00e-02 2.50e+03 ... (remaining 2860 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 159 2.37 - 3.00: 11702 3.00 - 3.63: 33752 3.63 - 4.27: 51080 4.27 - 4.90: 74096 Nonbonded interactions: 170789 Sorted by model distance: nonbonded pdb=" NH1 ARG E 63 " pdb=" C5' DA I 17 " model vdw 1.732 3.520 nonbonded pdb=" OE2 GLU A 59 " pdb=" O LEU A 60 " model vdw 1.840 3.040 nonbonded pdb=" O2 DC I 22 " pdb=" N1 DG J -21 " model vdw 1.851 2.496 nonbonded pdb=" O2 DT I 62 " pdb=" N1 DA J -62 " model vdw 1.868 2.496 nonbonded pdb=" NE ARG C 17 " pdb=" OP1 DT I -43 " model vdw 1.868 2.520 ... (remaining 170784 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 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and ((resid 20 through 24 and (name N or name CA or name C or name O \ or name CB )) or resid 25 through 102)) selection = (chain 'F' and resid 20 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } ncs_group { reference = chain 'N' selection = chain 'O' } 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=0.19 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.770 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 68.140 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.100 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 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 : 0.020 0.347 22077 Z= 1.253 Angle : 2.387 21.835 31168 Z= 1.545 Chirality : 0.121 0.784 3508 Planarity : 0.039 0.492 2863 Dihedral : 26.026 175.606 8852 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 68.74 Ramachandran Plot: Outliers : 1.63 % Allowed : 8.11 % Favored : 90.26 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.82 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -2.94 (0.16), residues: 1778 helix: -1.38 (0.14), residues: 885 sheet: -0.70 (0.49), residues: 96 loop : -2.77 (0.18), residues: 797 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 389 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 13 residues processed: 428 average time/residue: 0.3915 time to fit residues: 241.6158 Evaluate side-chains 254 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 241 time to evaluate : 1.901 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2397 time to fit residues: 7.8002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 84 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 188 optimal weight: 30.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN N 2 GLN N 25 ASN N 40 GLN ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 285 HIS ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 474 ASN ** W 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 579 GLN W 645 HIS ** W 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 756 HIS W 813 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.005 0.068 22077 Z= 0.314 Angle : 0.833 10.586 31168 Z= 0.459 Chirality : 0.046 0.218 3508 Planarity : 0.006 0.101 2863 Dihedral : 29.531 168.844 5205 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 23.48 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.83 % Favored : 95.66 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -1.48 (0.18), residues: 1778 helix: -0.07 (0.16), residues: 904 sheet: -1.10 (0.47), residues: 109 loop : -2.08 (0.20), residues: 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 328 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 331 average time/residue: 0.3887 time to fit residues: 187.4827 Evaluate side-chains 228 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 1.914 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2209 time to fit residues: 2.9069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 189 optimal weight: 8.9990 chunk 204 optimal weight: 0.3980 chunk 168 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 185 HIS ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 357 GLN ** W 536 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 557 ASN W 685 ASN ** W 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 22077 Z= 0.241 Angle : 0.709 8.929 31168 Z= 0.389 Chirality : 0.040 0.220 3508 Planarity : 0.005 0.043 2863 Dihedral : 29.129 177.968 5205 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.43 % Favored : 96.17 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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 (0.18), residues: 1778 helix: 0.24 (0.16), residues: 910 sheet: -0.77 (0.48), residues: 109 loop : -1.76 (0.20), residues: 759 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 296 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 297 average time/residue: 0.3992 time to fit residues: 173.8711 Evaluate side-chains 214 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.933 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 189 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 179 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 367 GLN W 557 ASN ** W 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 22077 Z= 0.234 Angle : 0.671 8.587 31168 Z= 0.370 Chirality : 0.038 0.206 3508 Planarity : 0.005 0.056 2863 Dihedral : 28.801 173.191 5205 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.17 % Favored : 95.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.92 (0.19), residues: 1778 helix: 0.19 (0.16), residues: 915 sheet: -0.37 (0.47), residues: 113 loop : -1.63 (0.21), residues: 750 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.3931 time to fit residues: 168.3477 Evaluate side-chains 212 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 2.9990 chunk 114 optimal weight: 50.0000 chunk 2 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 chunk 138 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 367 GLN ** W 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 739 GLN W1161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 22077 Z= 0.207 Angle : 0.637 9.704 31168 Z= 0.352 Chirality : 0.037 0.235 3508 Planarity : 0.005 0.054 2863 Dihedral : 28.587 175.294 5205 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.72 % Favored : 96.00 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.74 (0.19), residues: 1778 helix: 0.29 (0.17), residues: 916 sheet: -0.07 (0.47), residues: 113 loop : -1.51 (0.21), residues: 749 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 283 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 284 average time/residue: 0.3691 time to fit residues: 156.3956 Evaluate side-chains 209 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.911 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 0.9980 chunk 181 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 118 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 201 optimal weight: 20.0000 chunk 167 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 285 HIS ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.6396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 22077 Z= 0.196 Angle : 0.622 8.252 31168 Z= 0.342 Chirality : 0.037 0.203 3508 Planarity : 0.004 0.056 2863 Dihedral : 28.500 175.689 5205 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.60 % Favored : 96.11 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.19), residues: 1778 helix: 0.35 (0.17), residues: 913 sheet: 0.33 (0.46), residues: 126 loop : -1.45 (0.21), residues: 739 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 277 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 279 average time/residue: 0.3646 time to fit residues: 152.8834 Evaluate side-chains 217 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 2.008 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2429 time to fit residues: 3.1441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 114 optimal weight: 50.0000 chunk 146 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 200 optimal weight: 0.0170 chunk 125 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 overall best weight: 2.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN O 68 HIS ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 334 GLN ** W 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 557 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.113 22077 Z= 0.274 Angle : 0.681 9.285 31168 Z= 0.379 Chirality : 0.039 0.218 3508 Planarity : 0.005 0.057 2863 Dihedral : 28.605 174.868 5205 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.28 % Favored : 95.50 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.76 (0.19), residues: 1778 helix: 0.12 (0.17), residues: 910 sheet: 0.25 (0.45), residues: 131 loop : -1.38 (0.21), residues: 737 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 265 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 266 average time/residue: 0.3621 time to fit residues: 145.8637 Evaluate side-chains 199 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 1.968 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2400 time to fit residues: 2.9081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 136 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN W 177 HIS ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 367 GLN W 557 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.7149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 22077 Z= 0.185 Angle : 0.630 7.571 31168 Z= 0.347 Chirality : 0.038 0.224 3508 Planarity : 0.004 0.055 2863 Dihedral : 28.633 177.360 5205 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.66 % Favored : 96.11 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.19), residues: 1778 helix: 0.26 (0.17), residues: 912 sheet: 0.35 (0.46), residues: 130 loop : -1.32 (0.22), residues: 736 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.3534 time to fit residues: 143.9434 Evaluate side-chains 213 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.104 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 176 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 779 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.7448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 22077 Z= 0.227 Angle : 0.650 9.767 31168 Z= 0.361 Chirality : 0.038 0.243 3508 Planarity : 0.005 0.051 2863 Dihedral : 28.540 176.083 5205 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.17 % Favored : 95.61 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.19), residues: 1778 helix: 0.30 (0.17), residues: 891 sheet: 0.22 (0.45), residues: 135 loop : -1.29 (0.21), residues: 752 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.3595 time to fit residues: 141.2910 Evaluate side-chains 198 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.988 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 165 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 HIS ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 339 GLN W 547 ASN W 587 HIS W 779 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.8063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 22077 Z= 0.339 Angle : 0.758 9.336 31168 Z= 0.421 Chirality : 0.042 0.269 3508 Planarity : 0.006 0.070 2863 Dihedral : 28.951 176.260 5205 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 29.89 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.46 % Favored : 94.31 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 1778 helix: -0.13 (0.17), residues: 888 sheet: -0.32 (0.42), residues: 139 loop : -1.37 (0.22), residues: 751 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3556 Ramachandran restraints generated. 1778 Oldfield, 0 Emsley, 1778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.3540 time to fit residues: 132.9595 Evaluate side-chains 181 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 2.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 chunk 165 optimal weight: 0.0170 chunk 69 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 547 ASN W 779 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.093450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.058188 restraints weight = 217165.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.060536 restraints weight = 119415.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.061850 restraints weight = 82845.360| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.8117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 22077 Z= 0.189 Angle : 0.662 9.101 31168 Z= 0.363 Chirality : 0.039 0.227 3508 Planarity : 0.005 0.061 2863 Dihedral : 28.855 178.045 5205 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.77 % Favored : 96.00 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.19), residues: 1778 helix: 0.23 (0.17), residues: 886 sheet: 0.18 (0.48), residues: 119 loop : -1.28 (0.21), residues: 773 =============================================================================== Job complete usr+sys time: 4366.43 seconds wall clock time: 80 minutes 16.61 seconds (4816.61 seconds total)