Starting phenix.real_space_refine (version: dev) on Mon Dec 19 00:26:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/12_2022/7afl_11769_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/12_2022/7afl_11769.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/12_2022/7afl_11769_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/12_2022/7afl_11769_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/12_2022/7afl_11769_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/12_2022/7afl_11769.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/12_2022/7afl_11769.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/12_2022/7afl_11769_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/12_2022/7afl_11769_updated.pdb" } resolution = 4.2 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= 0.005 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 34322 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 22654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 22654 Classifications: {'RNA': 1054} Modifications used: {'rna2p_pur': 77, 'rna2p_pyr': 54, 'rna3p': 5, 'rna3p_pur': 530, 'rna3p_pyr': 388} Link IDs: {'rna2p': 131, 'rna3p': 922} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "V" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "X" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1174 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Unusual residues: {' MG': 25} Classifications: {'undetermined': 25} Link IDs: {None: 24} Time building chain proxies: 19.78, per 1000 atoms: 0.58 Number of scatterers: 34322 At special positions: 0 Unit cell: (145.39, 211.575, 139.965, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 1054 15.00 Mg 25 11.99 O 9438 8.00 N 6369 7.00 C 17386 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 24.28 Conformation dependent library (CDL) restraints added in 1.8 seconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 14 sheets defined 35.4% alpha, 15.3% beta 308 base pairs and 526 stacking pairs defined. Time for finding SS restraints: 18.84 Creating SS restraints... Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.900A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 50 through 64 Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 95 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 147 through 150 No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 153 through 160 removed outlier: 4.815A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.661A pdb=" N ALA E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 143 Processing helix chain 'E' and resid 150 through 157 Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'F' and resid 18 through 31 removed outlier: 3.734A pdb=" N ILE F 22 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 removed outlier: 4.046A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 105 removed outlier: 3.748A pdb=" N ALA F 105 " --> pdb=" O PRO F 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 101 through 105' Processing helix chain 'H' and resid 6 through 20 Processing helix chain 'H' and resid 31 through 42 Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'K' and resid 48 through 50 No H-bonds generated for 'chain 'K' and resid 48 through 50' Processing helix chain 'K' and resid 55 through 58 No H-bonds generated for 'chain 'K' and resid 55 through 58' Processing helix chain 'K' and resid 60 through 77 removed outlier: 4.037A pdb=" N ALA K 67 " --> pdb=" O ALA K 63 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG K 69 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 103 Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 117 Processing helix chain 'O' and resid 5 through 15 removed outlier: 3.543A pdb=" N GLU O 14 " --> pdb=" O LYS O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 45 removed outlier: 3.669A pdb=" N LEU O 31 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 71 removed outlier: 3.872A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN O 62 " --> pdb=" O ARG O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 84 Processing helix chain 'P' and resid 54 through 63 Processing helix chain 'P' and resid 69 through 81 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 13 through 16 No H-bonds generated for 'chain 'R' and resid 13 through 16' Processing helix chain 'R' and resid 26 through 31 Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'T' and resid 5 through 41 removed outlier: 3.665A pdb=" N LYS T 9 " --> pdb=" O LYS T 5 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG T 10 " --> pdb=" O SER T 6 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS T 16 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG T 24 " --> pdb=" O HIS T 20 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 63 Proline residue: T 56 - end of helix removed outlier: 3.513A pdb=" N ASP T 59 " --> pdb=" O GLN T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 86 Processing helix chain 'V' and resid 8 through 25 removed outlier: 4.707A pdb=" N GLN V 13 " --> pdb=" O GLN V 9 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU V 14 " --> pdb=" O ARG V 10 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS V 17 " --> pdb=" O GLN V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 47 No H-bonds generated for 'chain 'V' and resid 45 through 47' Processing helix chain 'V' and resid 62 through 74 removed outlier: 3.654A pdb=" N ALA V 67 " --> pdb=" O ASP V 63 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY V 68 " --> pdb=" O ALA V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 85 Processing helix chain 'X' and resid 5 through 19 removed outlier: 4.130A pdb=" N ALA X 14 " --> pdb=" O GLU X 10 " (cutoff:3.500A) Proline residue: X 15 - end of helix Processing helix chain 'X' and resid 48 through 65 removed outlier: 4.234A pdb=" N VAL X 64 " --> pdb=" O ALA X 60 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU X 65 " --> pdb=" O VAL X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 93 Processing sheet with id= A, first strand: chain 'D' and resid 123 through 125 Processing sheet with id= B, first strand: chain 'E' and resid 47 through 53 removed outlier: 3.548A pdb=" N THR E 37 " --> pdb=" O GLY E 49 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 85 through 88 Processing sheet with id= D, first strand: chain 'F' and resid 2 through 10 removed outlier: 3.643A pdb=" N VAL F 10 " --> pdb=" O HIS F 58 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 35 through 41 removed outlier: 3.545A pdb=" N LYS F 35 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU F 39 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU F 61 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 110 through 112 removed outlier: 5.677A pdb=" N SER H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE H 125 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 20 through 24 removed outlier: 4.348A pdb=" N VAL K 20 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE K 31 " --> pdb=" O HIS K 24 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 83 through 86 removed outlier: 6.795A pdb=" N ASN K 109 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL K 86 " --> pdb=" O ASN K 109 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR K 111 " --> pdb=" O VAL K 86 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'L' and resid 95 through 98 removed outlier: 4.874A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE L 82 " --> pdb=" O LYS L 30 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS L 30 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'P' and resid 3 through 5 removed outlier: 6.730A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Q' and resid 58 through 62 removed outlier: 16.048A pdb=" N THR Q 7 " --> pdb=" O PHE Q 28 " (cutoff:3.500A) removed outlier: 12.585A pdb=" N PHE Q 28 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'V' and resid 94 through 98 removed outlier: 6.181A pdb=" N THR V 55 " --> pdb=" O VAL V 38 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VAL V 38 " --> pdb=" O THR V 55 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'X' and resid 75 through 77 removed outlier: 6.135A pdb=" N ASP X 41 " --> pdb=" O LEU X 23 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU X 23 " --> pdb=" O ASP X 41 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'X' and resid 143 through 146 removed outlier: 6.894A pdb=" N THR X 126 " --> pdb=" O LYS X 118 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 695 hydrogen bonds 826 hydrogen bond angles 0 basepair planarities 308 basepair parallelities 526 stacking parallelities Total time for adding SS restraints: 25.09 Time building geometry restraints manager: 25.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5139 1.33 - 1.45: 15363 1.45 - 1.57: 14482 1.57 - 1.70: 2103 1.70 - 1.82: 88 Bond restraints: 37175 Sorted by residual: bond pdb=" O3' U A 571 " pdb=" P A A 572 " ideal model delta sigma weight residual 1.607 1.469 0.138 1.50e-02 4.44e+03 8.44e+01 bond pdb=" N3 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.500 1.347 0.153 2.00e-02 2.50e+03 5.82e+01 bond pdb=" C2 G7M A 527 " pdb=" N3 G7M A 527 " ideal model delta sigma weight residual 1.462 1.313 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" C2 2MG A1516 " pdb=" N2 2MG A1516 " ideal model delta sigma weight residual 1.481 1.340 0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C5 MA6 A1519 " pdb=" C4 MA6 A1519 " ideal model delta sigma weight residual 1.336 1.472 -0.136 2.00e-02 2.50e+03 4.62e+01 ... (remaining 37170 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.95: 5784 105.95 - 113.96: 23806 113.96 - 121.96: 17744 121.96 - 129.97: 7441 129.97 - 137.97: 668 Bond angle restraints: 55443 Sorted by residual: angle pdb=" N6 MA6 A1519 " pdb=" C6 MA6 A1519 " pdb=" N1 MA6 A1519 " ideal model delta sigma weight residual 98.71 121.40 -22.69 3.00e+00 1.11e-01 5.72e+01 angle pdb=" C ILE V 91 " pdb=" N VAL V 92 " pdb=" CA VAL V 92 " ideal model delta sigma weight residual 122.60 117.89 4.71 6.80e-01 2.16e+00 4.80e+01 angle pdb=" C LYS H 56 " pdb=" CA LYS H 56 " pdb=" CB LYS H 56 " ideal model delta sigma weight residual 111.00 116.99 -5.99 8.70e-01 1.32e+00 4.74e+01 angle pdb=" N6 MA6 A1518 " pdb=" C6 MA6 A1518 " pdb=" N1 MA6 A1518 " ideal model delta sigma weight residual 98.71 118.98 -20.27 3.00e+00 1.11e-01 4.56e+01 angle pdb=" C5 MA6 A1519 " pdb=" C6 MA6 A1519 " pdb=" N6 MA6 A1519 " ideal model delta sigma weight residual 140.50 121.53 18.97 3.00e+00 1.11e-01 4.00e+01 ... (remaining 55438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 18788 35.61 - 71.23: 1028 71.23 - 106.84: 92 106.84 - 142.45: 10 142.45 - 178.07: 5 Dihedral angle restraints: 19923 sinusoidal: 15653 harmonic: 4270 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 46.47 153.53 1 1.50e+01 4.44e-03 8.09e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 51.18 148.82 1 1.50e+01 4.44e-03 7.92e+01 dihedral pdb=" O4' C A 183 " pdb=" C1' C A 183 " pdb=" N1 C A 183 " pdb=" C2 C A 183 " ideal model delta sinusoidal sigma weight residual -128.00 50.07 -178.07 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 19920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 5946 0.082 - 0.164: 861 0.164 - 0.246: 214 0.246 - 0.327: 27 0.327 - 0.409: 6 Chirality restraints: 7054 Sorted by residual: chirality pdb=" CA ASN D 89 " pdb=" N ASN D 89 " pdb=" C ASN D 89 " pdb=" CB ASN D 89 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA ASN T 52 " pdb=" N ASN T 52 " pdb=" C ASN T 52 " pdb=" CB ASN T 52 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA VAL K 32 " pdb=" N VAL K 32 " pdb=" C VAL K 32 " pdb=" CB VAL K 32 " both_signs ideal model delta sigma weight residual False 2.44 2.81 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 7051 not shown) Planarity restraints: 3113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " 0.060 2.00e-02 2.50e+03 5.84e-01 7.69e+03 pdb=" C4' 2MG A1516 " 0.432 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " 0.571 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.632 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " -0.170 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " 0.978 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " 0.230 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " -0.877 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG A1516 " 0.096 2.00e-02 2.50e+03 1.84e-01 1.10e+03 pdb=" N9 2MG A1516 " 0.009 2.00e-02 2.50e+03 pdb=" C8 2MG A1516 " -0.089 2.00e-02 2.50e+03 pdb=" N7 2MG A1516 " -0.121 2.00e-02 2.50e+03 pdb=" C5 2MG A1516 " -0.035 2.00e-02 2.50e+03 pdb=" C6 2MG A1516 " -0.011 2.00e-02 2.50e+03 pdb=" O6 2MG A1516 " -0.086 2.00e-02 2.50e+03 pdb=" N1 2MG A1516 " 0.093 2.00e-02 2.50e+03 pdb=" C2 2MG A1516 " 0.182 2.00e-02 2.50e+03 pdb=" N2 2MG A1516 " 0.265 2.00e-02 2.50e+03 pdb=" N3 2MG A1516 " 0.157 2.00e-02 2.50e+03 pdb=" C4 2MG A1516 " 0.053 2.00e-02 2.50e+03 pdb=" CM2 2MG A1516 " -0.512 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " 0.134 2.00e-02 2.50e+03 2.18e-01 4.76e+02 pdb=" N6 MA6 A1519 " -0.378 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " 0.122 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " 0.122 2.00e-02 2.50e+03 ... (remaining 3110 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 648 2.46 - 3.07: 26349 3.07 - 3.68: 78460 3.68 - 4.29: 102394 4.29 - 4.90: 134557 Nonbonded interactions: 342408 Sorted by model distance: nonbonded pdb=" OP2 A A 116 " pdb="MG MG A1625 " model vdw 1.852 2.170 nonbonded pdb=" OP2 A A 53 " pdb="MG MG A1613 " model vdw 1.883 2.170 nonbonded pdb=" OP2 G A 289 " pdb="MG MG A1625 " model vdw 1.890 2.170 nonbonded pdb=" O3' C A1521 " pdb="MG MG A1622 " model vdw 1.899 2.170 nonbonded pdb=" OP1 A A 547 " pdb="MG MG A1614 " model vdw 1.909 2.170 ... (remaining 342403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1054 5.49 5 Mg 25 5.21 5 S 50 5.16 5 C 17386 2.51 5 N 6369 2.21 5 O 9438 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 14.930 Check model and map are aligned: 0.530 Convert atoms to be neutral: 0.290 Process input model: 121.850 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 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 : 0.010 0.153 37175 Z= 0.618 Angle : 1.084 22.687 55443 Z= 0.677 Chirality : 0.065 0.409 7054 Planarity : 0.013 0.584 3113 Dihedral : 17.440 178.066 17165 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 43.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.20), residues: 1458 helix: -0.77 (0.23), residues: 495 sheet: -1.05 (0.32), residues: 250 loop : -1.55 (0.21), residues: 713 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 2.251 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 outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.5736 time to fit residues: 366.2104 Evaluate side-chains 242 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 2.335 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 chunk 193 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN E 70 ASN E 73 ASN E 83 HIS ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 ASN L 5 ASN L 72 HIS O 37 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 ASN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN R 52 GLN T 20 HIS ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 37175 Z= 0.284 Angle : 0.705 13.110 55443 Z= 0.363 Chirality : 0.038 0.272 7054 Planarity : 0.006 0.122 3113 Dihedral : 17.056 179.283 14262 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 34.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.21), residues: 1458 helix: -0.72 (0.21), residues: 526 sheet: -0.74 (0.30), residues: 276 loop : -1.11 (0.24), residues: 656 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 2.131 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: 1 outliers final: 1 residues processed: 315 average time/residue: 0.5173 time to fit residues: 252.6536 Evaluate side-chains 219 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 218 time to evaluate : 2.042 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2999 time to fit residues: 2.8257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 chunk 152 optimal weight: 30.0000 chunk 61 optimal weight: 10.0000 chunk 224 optimal weight: 0.9980 chunk 242 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 ASN P 9 HIS ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 47 ASN ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 37175 Z= 0.324 Angle : 0.682 12.188 55443 Z= 0.352 Chirality : 0.038 0.244 7054 Planarity : 0.006 0.124 3113 Dihedral : 16.922 179.957 14262 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 37.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.21), residues: 1458 helix: -0.56 (0.20), residues: 524 sheet: -1.04 (0.28), residues: 304 loop : -1.06 (0.25), residues: 630 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 292 time to evaluate : 1.918 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 outliers start: 5 outliers final: 2 residues processed: 296 average time/residue: 0.5130 time to fit residues: 236.4901 Evaluate side-chains 214 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 212 time to evaluate : 1.912 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2760 time to fit residues: 3.0734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 225 optimal weight: 9.9990 chunk 238 optimal weight: 0.4980 chunk 117 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN ** E 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 ASN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN V 73 GLN ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 37175 Z= 0.157 Angle : 0.576 11.492 55443 Z= 0.301 Chirality : 0.033 0.277 7054 Planarity : 0.005 0.119 3113 Dihedral : 16.317 179.330 14262 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1458 helix: -0.22 (0.21), residues: 523 sheet: -0.92 (0.28), residues: 299 loop : -0.86 (0.25), residues: 636 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 309 time to evaluate : 2.084 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 outliers start: 3 outliers final: 1 residues processed: 311 average time/residue: 0.5304 time to fit residues: 255.9281 Evaluate side-chains 218 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 2.146 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3526 time to fit residues: 2.8908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 177 optimal weight: 0.1980 chunk 98 optimal weight: 20.0000 chunk 203 optimal weight: 0.8980 chunk 165 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN V 73 GLN ** X 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 37175 Z= 0.174 Angle : 0.554 11.648 55443 Z= 0.291 Chirality : 0.032 0.262 7054 Planarity : 0.005 0.119 3113 Dihedral : 16.100 178.579 14262 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 26.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.21), residues: 1458 helix: 0.05 (0.22), residues: 527 sheet: -0.75 (0.30), residues: 275 loop : -0.79 (0.25), residues: 656 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 293 time to evaluate : 2.136 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: 2 outliers final: 0 residues processed: 295 average time/residue: 0.5262 time to fit residues: 240.6978 Evaluate side-chains 211 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.083 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 20.0000 chunk 215 optimal weight: 0.4980 chunk 47 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 238 optimal weight: 30.0000 chunk 198 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 overall best weight: 8.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 HIS ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 37175 Z= 0.365 Angle : 0.705 13.800 55443 Z= 0.364 Chirality : 0.038 0.275 7054 Planarity : 0.006 0.121 3113 Dihedral : 16.591 179.322 14262 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 41.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.21), residues: 1458 helix: -0.32 (0.21), residues: 530 sheet: -0.92 (0.30), residues: 258 loop : -0.84 (0.25), residues: 670 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 2.402 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 outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.4905 time to fit residues: 199.5440 Evaluate side-chains 192 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.130 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 174 optimal weight: 0.0770 chunk 135 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 238 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 109 optimal weight: 20.0000 overall best weight: 5.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 37175 Z= 0.259 Angle : 0.618 11.998 55443 Z= 0.322 Chirality : 0.035 0.277 7054 Planarity : 0.005 0.120 3113 Dihedral : 16.474 179.030 14262 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 34.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1458 helix: -0.23 (0.21), residues: 527 sheet: -0.96 (0.30), residues: 276 loop : -0.78 (0.25), residues: 655 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.019 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 outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.4821 time to fit residues: 201.3262 Evaluate side-chains 192 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.062 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 151 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 GLN ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 37175 Z= 0.198 Angle : 0.586 11.913 55443 Z= 0.306 Chirality : 0.033 0.278 7054 Planarity : 0.005 0.119 3113 Dihedral : 16.261 178.845 14262 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 29.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.22), residues: 1458 helix: -0.02 (0.22), residues: 526 sheet: -0.84 (0.30), residues: 275 loop : -0.81 (0.25), residues: 657 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 2.078 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 outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.5088 time to fit residues: 218.3009 Evaluate side-chains 198 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 2.281 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 96 optimal weight: 20.0000 chunk 174 optimal weight: 0.0070 chunk 68 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 209 optimal weight: 20.0000 chunk 145 optimal weight: 0.8980 chunk 234 optimal weight: 10.0000 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 37175 Z= 0.156 Angle : 0.564 11.782 55443 Z= 0.297 Chirality : 0.032 0.274 7054 Planarity : 0.005 0.118 3113 Dihedral : 15.996 178.519 14262 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1458 helix: -0.02 (0.22), residues: 531 sheet: -0.78 (0.30), residues: 270 loop : -0.83 (0.24), residues: 657 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.190 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 outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.5018 time to fit residues: 221.6115 Evaluate side-chains 203 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.297 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 chunk 195 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 151 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 208 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 37175 Z= 0.278 Angle : 0.626 12.245 55443 Z= 0.327 Chirality : 0.035 0.283 7054 Planarity : 0.005 0.119 3113 Dihedral : 16.177 179.907 14262 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 35.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.22), residues: 1458 helix: -0.14 (0.22), residues: 527 sheet: -0.91 (0.30), residues: 272 loop : -0.80 (0.25), residues: 659 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.189 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 outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.5007 time to fit residues: 207.6804 Evaluate side-chains 193 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.064 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 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 = 0.2688 r_free = 0.2688 target = 0.024162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.019904 restraints weight = 537222.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.020638 restraints weight = 230208.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.021088 restraints weight = 133009.905| |-----------------------------------------------------------------------------| r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 37175 Z= 0.371 Angle : 0.719 16.715 55443 Z= 0.371 Chirality : 0.038 0.294 7054 Planarity : 0.006 0.120 3113 Dihedral : 16.556 179.961 14262 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 42.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.21), residues: 1458 helix: -0.55 (0.21), residues: 531 sheet: -1.14 (0.30), residues: 273 loop : -1.05 (0.24), residues: 654 =============================================================================== Job complete usr+sys time: 5211.55 seconds wall clock time: 97 minutes 54.72 seconds (5874.72 seconds total)