Starting phenix.real_space_refine (version: dev) on Sat May 14 00:06:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfe_8827/05_2022/5wfe_8827.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfe_8827/05_2022/5wfe_8827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfe_8827/05_2022/5wfe_8827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfe_8827/05_2022/5wfe_8827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfe_8827/05_2022/5wfe_8827.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wfe_8827/05_2022/5wfe_8827.pdb" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.081 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 "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C ARG 131": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 138": "NH1" <-> "NH2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 15523 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2018 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain breaks: 1 Chain: "B" Number of atoms: 2157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2157 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 17, 'TRANS': 261} Chain: "C" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1964 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Chain: "D" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2096 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 15, 'TRANS': 256} Chain: "E" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "F" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "G" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 578 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 907 Classifications: {'DNA': 45} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 44} Chain: "I" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1570 Classifications: {'DNA': 77} Link IDs: {'rna3p': 76} Chain: "J" Number of atoms: 1244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1244 Classifications: {'DNA': 60} Link IDs: {'rna3p': 59} Chain: "K" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 769 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 742 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 8.36, per 1000 atoms: 0.54 Number of scatterers: 15523 At special positions: 0 Unit cell: (120.91, 128.4, 196.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 208 15.00 O 3284 8.00 N 2771 7.00 C 9220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.62 Conformation dependent library (CDL) restraints added in 1.7 seconds 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 9 sheets defined 54.1% alpha, 14.9% beta 94 base pairs and 161 stacking pairs defined. Time for finding SS restraints: 5.91 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 83 Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 108 through 124 Processing helix chain 'A' and resid 133 through 157 Processing helix chain 'A' and resid 175 through 199 Processing helix chain 'A' and resid 213 through 223 removed outlier: 3.756A pdb=" N ILE A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 242 through 259 removed outlier: 3.790A pdb=" N GLU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 removed outlier: 4.409A pdb=" N ILE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Proline residue: A 266 - end of helix Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 62 through 71 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 95 through 108 removed outlier: 4.121A pdb=" N LEU B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 124 Processing helix chain 'B' and resid 133 through 157 Processing helix chain 'B' and resid 166 through 170 removed outlier: 3.592A pdb=" N ASP B 169 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 199 Processing helix chain 'B' and resid 213 through 239 removed outlier: 3.984A pdb=" N ILE B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N PHE B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 242 through 259 removed outlier: 3.521A pdb=" N GLU B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 274 removed outlier: 4.136A pdb=" N ILE B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Proline residue: B 266 - end of helix removed outlier: 3.757A pdb=" N ALA B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 80 through 83 Processing helix chain 'C' and resid 95 through 108 removed outlier: 3.670A pdb=" N LEU C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 124 Processing helix chain 'C' and resid 133 through 156 Processing helix chain 'C' and resid 175 through 199 Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.883A pdb=" N ILE C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 242 through 259 removed outlier: 3.630A pdb=" N GLU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 274 removed outlier: 4.505A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Proline residue: C 266 - end of helix Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.595A pdb=" N ARG D 14 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 62 through 71 Processing helix chain 'D' and resid 80 through 82 No H-bonds generated for 'chain 'D' and resid 80 through 82' Processing helix chain 'D' and resid 95 through 108 removed outlier: 3.766A pdb=" N ASP D 108 " --> pdb=" O LYS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 125 Processing helix chain 'D' and resid 133 through 157 removed outlier: 3.536A pdb=" N LEU D 137 " --> pdb=" O SER D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.566A pdb=" N ASP D 169 " --> pdb=" O ASP D 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP D 170 " --> pdb=" O PRO D 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 166 through 170' Processing helix chain 'D' and resid 175 through 199 Processing helix chain 'D' and resid 213 through 239 removed outlier: 3.764A pdb=" N ILE D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL D 229 " --> pdb=" O PHE D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 242 through 259 removed outlier: 3.971A pdb=" N GLU D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.986A pdb=" N LYS D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Proline residue: D 266 - end of helix removed outlier: 4.043A pdb=" N ALA D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 23 removed outlier: 3.735A pdb=" N ARG E 16 " --> pdb=" O PRO E 12 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 51 removed outlier: 3.523A pdb=" N ALA E 51 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 23 removed outlier: 3.634A pdb=" N ARG F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TRP F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 51 Processing helix chain 'K' and resid 4 through 17 Processing helix chain 'K' and resid 19 through 40 removed outlier: 3.514A pdb=" N VAL K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 93 removed outlier: 4.225A pdb=" N ASN K 93 " --> pdb=" O SER K 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 14 removed outlier: 3.727A pdb=" N ARG L 9 " --> pdb=" O GLU L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 39 Processing helix chain 'L' and resid 83 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 5.809A pdb=" N ILE A 18 " --> pdb=" O MET A 53 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU A 75 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 88 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 89 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU B 74 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL B 15 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE B 52 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N MET B 17 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 9.804A pdb=" N LEU B 54 " --> pdb=" O MET B 17 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N PHE B 19 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 35 removed outlier: 7.215A pdb=" N ILE A 25 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL B 27 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS B 43 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL E 89 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 20 removed outlier: 6.093A pdb=" N ILE C 18 " --> pdb=" O MET C 53 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LEU C 75 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 75 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N SER D 16 " --> pdb=" O CYS D 51 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N MET D 53 " --> pdb=" O SER D 16 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE D 18 " --> pdb=" O MET D 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 32 through 35 removed outlier: 7.472A pdb=" N ILE C 25 " --> pdb=" O SER C 61 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL D 27 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS D 43 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL F 89 " --> pdb=" O HIS D 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 24 through 27 removed outlier: 3.707A pdb=" N VAL E 26 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N MET E 3 " --> pdb=" O ALA E 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.836A pdb=" N VAL F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N MET F 3 " --> pdb=" O ALA F 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 44 through 46 removed outlier: 3.734A pdb=" N ARG K 76 " --> pdb=" O LYS K 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 43 through 45 removed outlier: 4.049A pdb=" N LYS L 75 " --> pdb=" O ARG L 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 60 through 62 666 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 221 hydrogen bonds 432 hydrogen bond angles 0 basepair planarities 94 basepair parallelities 161 stacking parallelities Total time for adding SS restraints: 5.94 Time building geometry restraints manager: 8.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3566 1.33 - 1.45: 4073 1.45 - 1.57: 8138 1.57 - 1.69: 414 1.69 - 1.81: 64 Bond restraints: 16255 Sorted by residual: bond pdb=" N LYS F 38 " pdb=" CA LYS F 38 " ideal model delta sigma weight residual 1.457 1.407 0.050 1.29e-02 6.01e+03 1.52e+01 bond pdb=" C ALA F 37 " pdb=" N LYS F 38 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.40e-02 5.10e+03 6.27e+00 bond pdb=" C3' DG I 6 " pdb=" O3' DG I 6 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.31e+00 bond pdb=" C GLN A 90 " pdb=" O GLN A 90 " ideal model delta sigma weight residual 1.233 1.224 0.009 4.80e-03 4.34e+04 3.19e+00 bond pdb=" C3' DC H 37 " pdb=" O3' DC H 37 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.03e+00 ... (remaining 16250 not shown) Histogram of bond angle deviations from ideal: 97.56 - 104.84: 1063 104.84 - 112.13: 8661 112.13 - 119.42: 4939 119.42 - 126.70: 7506 126.70 - 133.99: 749 Bond angle restraints: 22918 Sorted by residual: angle pdb=" C ALA F 37 " pdb=" N LYS F 38 " pdb=" CA LYS F 38 " ideal model delta sigma weight residual 121.54 115.20 6.34 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C GLU E 52 " pdb=" CA GLU E 52 " pdb=" CB GLU E 52 " ideal model delta sigma weight residual 114.40 110.60 3.80 1.25e+00 6.40e-01 9.24e+00 angle pdb=" C ALA B 273 " pdb=" N ALA B 274 " pdb=" CA ALA B 274 " ideal model delta sigma weight residual 120.38 124.68 -4.30 1.46e+00 4.69e-01 8.67e+00 angle pdb=" C3' DC H 37 " pdb=" O3' DC H 37 " pdb=" P DG H 38 " ideal model delta sigma weight residual 120.20 124.58 -4.38 1.50e+00 4.44e-01 8.53e+00 angle pdb=" C3' DT J 33 " pdb=" C2' DT J 33 " pdb=" C1' DT J 33 " ideal model delta sigma weight residual 101.60 97.56 4.04 1.50e+00 4.44e-01 7.26e+00 ... (remaining 22913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 8023 34.61 - 69.23: 958 69.23 - 103.84: 27 103.84 - 138.45: 2 138.45 - 173.07: 6 Dihedral angle restraints: 9016 sinusoidal: 4886 harmonic: 4130 Sorted by residual: dihedral pdb=" CA ARG B 95 " pdb=" C ARG B 95 " pdb=" N SER B 96 " pdb=" CA SER B 96 " ideal model delta harmonic sigma weight residual -180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" C4' DC I 17 " pdb=" C3' DC I 17 " pdb=" O3' DC I 17 " pdb=" P DA I 18 " ideal model delta sinusoidal sigma weight residual -140.00 33.07 -173.07 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT H 28 " pdb=" C3' DT H 28 " pdb=" O3' DT H 28 " pdb=" P DG H 29 " ideal model delta sinusoidal sigma weight residual 220.00 48.62 171.38 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 9013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1653 0.031 - 0.062: 664 0.062 - 0.093: 192 0.093 - 0.125: 83 0.125 - 0.156: 10 Chirality restraints: 2602 Sorted by residual: chirality pdb=" P DG H 38 " pdb=" OP1 DG H 38 " pdb=" OP2 DG H 38 " pdb=" O5' DG H 38 " both_signs ideal model delta sigma weight residual True 2.35 -2.50 -0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CB ILE B 176 " pdb=" CA ILE B 176 " pdb=" CG1 ILE B 176 " pdb=" CG2 ILE B 176 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.68e-01 chirality pdb=" C1' DT J 33 " pdb=" O4' DT J 33 " pdb=" C2' DT J 33 " pdb=" N1 DT J 33 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 2599 not shown) Planarity restraints: 2209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 166 " 0.047 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO A 167 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 167 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 167 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 45 " -0.024 2.00e-02 2.50e+03 1.21e-02 4.02e+00 pdb=" N9 DA I 45 " 0.030 2.00e-02 2.50e+03 pdb=" C8 DA I 45 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 45 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 45 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 45 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA I 45 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DA I 45 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA I 45 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 45 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 45 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 38 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C LYS F 38 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS F 38 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE F 39 " 0.010 2.00e-02 2.50e+03 ... (remaining 2206 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 95 2.49 - 3.09: 10815 3.09 - 3.70: 27152 3.70 - 4.30: 37948 4.30 - 4.90: 56901 Nonbonded interactions: 132911 Sorted by model distance: nonbonded pdb=" N3 DT J 29 " pdb=" CB PRO L 64 " model vdw 1.891 3.520 nonbonded pdb=" O2 DC I 32 " pdb=" N2 DG J 41 " model vdw 2.018 2.496 nonbonded pdb=" N2 DG H 38 " pdb=" O2 DC I 10 " model vdw 2.023 2.496 nonbonded pdb=" C2 DT J 29 " pdb=" CB PRO L 64 " model vdw 2.091 3.660 nonbonded pdb=" N7 DG I 57 " pdb=" N4 DC I 58 " model vdw 2.118 2.600 ... (remaining 132906 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 16 through 167 or resid 174 through 275)) selection = (chain 'B' and (resid 16 through 167 or resid 174 through 275)) selection = (chain 'C' and resid 16 through 275) selection = (chain 'D' and (resid 16 through 167 or resid 174 through 275)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 5 Type Number sf(0) Gaussians P 208 5.49 5 S 40 5.16 5 C 9220 2.51 5 N 2771 2.21 5 O 3284 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: 1.240 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: 6.700 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.110 Process input model: 47.360 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 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 : 0.004 0.055 16255 Z= 0.215 Angle : 0.661 9.228 22918 Z= 0.395 Chirality : 0.039 0.156 2602 Planarity : 0.005 0.072 2209 Dihedral : 22.675 173.065 6364 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.63 % Favored : 95.30 % Rotamer Outliers : 0.09 % 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: -1.79 (0.19), residues: 1427 helix: -0.66 (0.16), residues: 707 sheet: -0.64 (0.31), residues: 235 loop : -2.08 (0.24), residues: 485 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 417 time to evaluate : 1.390 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: 418 average time/residue: 0.3431 time to fit residues: 197.1878 Evaluate side-chains 211 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.439 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 278 GLN B 155 GLN B 177 ASN C 90 GLN C 178 GLN D 7 ASN E 10 ASN K 59 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.080 16255 Z= 0.613 Angle : 0.920 17.458 22918 Z= 0.492 Chirality : 0.049 0.249 2602 Planarity : 0.008 0.124 2209 Dihedral : 28.587 179.866 3685 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 26.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.48 % Favored : 95.37 % Rotamer Outliers : 4.43 % 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: -1.15 (0.21), residues: 1427 helix: 0.02 (0.18), residues: 716 sheet: -0.50 (0.31), residues: 242 loop : -2.00 (0.27), residues: 469 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 215 time to evaluate : 1.475 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: 52 outliers final: 33 residues processed: 247 average time/residue: 0.3147 time to fit residues: 108.6411 Evaluate side-chains 206 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1494 time to fit residues: 10.6248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 16255 Z= 0.235 Angle : 0.699 10.848 22918 Z= 0.381 Chirality : 0.041 0.220 2602 Planarity : 0.006 0.111 2209 Dihedral : 28.522 178.683 3685 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 1.53 % 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: -0.28 (0.21), residues: 1427 helix: 0.83 (0.18), residues: 717 sheet: -0.16 (0.34), residues: 217 loop : -1.68 (0.26), residues: 493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 224 time to evaluate : 1.441 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: 18 outliers final: 4 residues processed: 235 average time/residue: 0.3204 time to fit residues: 105.4693 Evaluate side-chains 196 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1416 time to fit residues: 3.0080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 146 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 16255 Z= 0.262 Angle : 0.691 10.561 22918 Z= 0.376 Chirality : 0.041 0.191 2602 Planarity : 0.005 0.080 2209 Dihedral : 28.342 178.351 3685 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 2.39 % 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: -0.03 (0.21), residues: 1427 helix: 1.09 (0.19), residues: 718 sheet: -0.09 (0.35), residues: 191 loop : -1.56 (0.26), residues: 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 213 time to evaluate : 1.523 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: 28 outliers final: 16 residues processed: 225 average time/residue: 0.3063 time to fit residues: 97.2106 Evaluate side-chains 202 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 1.524 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1406 time to fit residues: 6.0668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 106 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 16255 Z= 0.262 Angle : 0.689 10.480 22918 Z= 0.373 Chirality : 0.040 0.157 2602 Planarity : 0.005 0.064 2209 Dihedral : 28.258 179.152 3685 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 1.71 % 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: 0.07 (0.22), residues: 1427 helix: 1.18 (0.18), residues: 719 sheet: -0.22 (0.35), residues: 210 loop : -1.51 (0.27), residues: 498 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 207 time to evaluate : 1.501 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: 20 outliers final: 6 residues processed: 214 average time/residue: 0.2899 time to fit residues: 89.6695 Evaluate side-chains 194 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 1.432 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1367 time to fit residues: 3.3290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 38 optimal weight: 0.0010 chunk 154 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 16255 Z= 0.271 Angle : 0.690 14.963 22918 Z= 0.371 Chirality : 0.041 0.287 2602 Planarity : 0.005 0.052 2209 Dihedral : 28.171 179.221 3685 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 1.79 % 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: 0.11 (0.22), residues: 1427 helix: 1.26 (0.19), residues: 719 sheet: -0.22 (0.37), residues: 184 loop : -1.49 (0.26), residues: 524 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 195 time to evaluate : 1.520 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 outliers start: 21 outliers final: 8 residues processed: 203 average time/residue: 0.3149 time to fit residues: 90.9476 Evaluate side-chains 191 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 183 time to evaluate : 1.511 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1836 time to fit residues: 4.3808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 9.9990 chunk 17 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 113 optimal weight: 0.2980 chunk 87 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 154 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 GLN F 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 16255 Z= 0.234 Angle : 0.676 12.262 22918 Z= 0.364 Chirality : 0.040 0.202 2602 Planarity : 0.004 0.037 2209 Dihedral : 28.109 179.921 3685 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 1.11 % 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: 0.26 (0.22), residues: 1427 helix: 1.36 (0.19), residues: 715 sheet: -0.06 (0.39), residues: 179 loop : -1.40 (0.26), residues: 533 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 200 time to evaluate : 1.510 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: 13 outliers final: 6 residues processed: 205 average time/residue: 0.3033 time to fit residues: 88.8370 Evaluate side-chains 187 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 181 time to evaluate : 1.444 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1460 time to fit residues: 3.4555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 16255 Z= 0.264 Angle : 0.696 13.352 22918 Z= 0.371 Chirality : 0.040 0.158 2602 Planarity : 0.004 0.040 2209 Dihedral : 28.064 179.718 3685 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 1.02 % 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: 0.25 (0.22), residues: 1427 helix: 1.33 (0.19), residues: 717 sheet: -0.18 (0.36), residues: 207 loop : -1.36 (0.27), residues: 503 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 182 time to evaluate : 1.469 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 outliers start: 12 outliers final: 7 residues processed: 187 average time/residue: 0.3008 time to fit residues: 81.0197 Evaluate side-chains 179 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 172 time to evaluate : 1.474 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1817 time to fit residues: 3.9630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 135 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 10 ASN L 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.065 16255 Z= 0.479 Angle : 0.806 12.601 22918 Z= 0.429 Chirality : 0.044 0.158 2602 Planarity : 0.006 0.070 2209 Dihedral : 28.088 178.728 3685 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 1.11 % 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: -0.33 (0.22), residues: 1427 helix: 0.81 (0.18), residues: 719 sheet: -0.18 (0.35), residues: 233 loop : -1.79 (0.27), residues: 475 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 176 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 182 average time/residue: 0.3092 time to fit residues: 82.6510 Evaluate side-chains 171 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 165 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1463 time to fit residues: 3.4488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 146 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 16255 Z= 0.238 Angle : 0.714 11.515 22918 Z= 0.379 Chirality : 0.040 0.171 2602 Planarity : 0.005 0.073 2209 Dihedral : 28.093 177.923 3685 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 0.17 % 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: 0.23 (0.22), residues: 1427 helix: 1.28 (0.19), residues: 717 sheet: -0.17 (0.36), residues: 210 loop : -1.35 (0.28), residues: 500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2854 Ramachandran restraints generated. 1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 1.797 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 outliers start: 2 outliers final: 1 residues processed: 183 average time/residue: 0.3168 time to fit residues: 83.9703 Evaluate side-chains 173 residues out of total 1175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.490 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7037 time to fit residues: 2.6897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.118722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.087510 restraints weight = 50869.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.088738 restraints weight = 26484.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.089409 restraints weight = 16956.764| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 16255 Z= 0.207 Angle : 0.690 11.543 22918 Z= 0.370 Chirality : 0.040 0.164 2602 Planarity : 0.004 0.076 2209 Dihedral : 27.957 179.562 3685 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 0.60 % 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: 0.51 (0.22), residues: 1427 helix: 1.50 (0.19), residues: 718 sheet: -0.00 (0.35), residues: 208 loop : -1.21 (0.28), residues: 501 =============================================================================== Job complete usr+sys time: 2867.29 seconds wall clock time: 52 minutes 57.77 seconds (3177.77 seconds total)