Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 05:02:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phr_13427/04_2023/7phr_13427.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phr_13427/04_2023/7phr_13427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phr_13427/04_2023/7phr_13427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phr_13427/04_2023/7phr_13427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phr_13427/04_2023/7phr_13427.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phr_13427/04_2023/7phr_13427.pdb" } resolution = 3.08 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 7304 2.51 5 N 1939 2.21 5 O 2207 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11511 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1898 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 235} Chain: "B" Number of atoms: 2252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2252 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 269} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 872 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 111} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 104} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 950 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 117} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2246 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 263} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "P" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 69 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 6} Chain: "Z" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 275 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "e" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 979 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 118} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "z" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.17, per 1000 atoms: 0.54 Number of scatterers: 11511 At special positions: 0 Unit cell: (85.05, 91.35, 194.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 2207 8.00 N 1939 7.00 C 7304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 90 " distance=2.01 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 209 " distance=2.02 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 82 " - pdb=" SG CYS C 85 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 52 " distance=2.03 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 75 " distance=2.04 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 203 " - pdb=" SG CYS H 259 " distance=2.03 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 80 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 11 " - pdb=" SG CYS z 11 " distance=2.03 Simple disulfide: pdb=" SG CYS e 27 " - pdb=" SG CYS e 76 " distance=2.03 Simple disulfide: pdb=" SG CYS e 97 " - pdb=" SG CYS e 100 " distance=2.03 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 Links applied NAG-ASN " NAG A 301 " - " ASN A 23 " " NAG A 302 " - " ASN A 143 " " NAG A 303 " - " ASN A 177 " " NAG B 301 " - " ASN B 19 " " NAG D 401 " - " ASN D 17 " " NAG D 402 " - " ASN D 53 " Time building additional restraints: 4.22 Conformation dependent library (CDL) restraints added in 1.6 seconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 25 sheets defined 26.6% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.987A pdb=" N THR A 85 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 removed outlier: 4.655A pdb=" N ASN A 189 " --> pdb=" O ALA A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 217 through 250 Processing helix chain 'B' and resid 115 through 119 removed outlier: 3.527A pdb=" N LYS B 118 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 247 through 286 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 89 through 116 Processing helix chain 'D' and resid 57 through 60 Processing helix chain 'D' and resid 79 through 107 Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 104 through 132 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 137 through 150 Processing helix chain 'H' and resid 151 through 162 Processing helix chain 'H' and resid 162 through 175 Processing helix chain 'H' and resid 175 through 180 Processing helix chain 'H' and resid 253 through 255 No H-bonds generated for 'chain 'H' and resid 253 through 255' Processing helix chain 'Z' and resid 3 through 6 Processing helix chain 'Z' and resid 7 through 34 removed outlier: 3.974A pdb=" N CYS Z 11 " --> pdb=" O ASP Z 7 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU Z 14 " --> pdb=" O LEU Z 10 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU Z 18 " --> pdb=" O LEU Z 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 86 Processing helix chain 'e' and resid 104 through 134 Processing helix chain 'z' and resid 7 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 15 removed outlier: 6.488A pdb=" N LEU A 12 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE A 109 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE A 14 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 33 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 25 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 121 removed outlier: 6.061A pdb=" N ASN A 170 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 121 removed outlier: 6.061A pdb=" N ASN A 170 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 8 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 15 removed outlier: 6.667A pdb=" N MET B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR B 49 " --> pdb=" O MET B 33 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP B 35 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASP B 39 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY B 43 " --> pdb=" O ASP B 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 15 Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 127 removed outlier: 5.297A pdb=" N THR B 141 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL B 195 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL B 143 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU B 193 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU B 145 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N SER B 191 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR B 147 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU B 189 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 165 removed outlier: 4.682A pdb=" N TRP B 158 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 9 through 12 removed outlier: 4.116A pdb=" N LEU C 21 " --> pdb=" O TYR C 12 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL C 20 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 38 through 43 removed outlier: 6.648A pdb=" N TRP C 33 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE C 42 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE C 31 " --> pdb=" O PHE C 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 79 removed outlier: 3.811A pdb=" N TRP e 37 " --> pdb=" O ILE e 44 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 87 Processing sheet with id=AB5, first strand: chain 'D' and resid 5 through 8 removed outlier: 5.944A pdb=" N VAL D 12 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 21 through 25 removed outlier: 6.573A pdb=" N ILE D 49 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N TYR E 89 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR D 64 " --> pdb=" O TYR E 89 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TYR E 91 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLN D 66 " --> pdb=" O TYR E 91 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ARG E 93 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N HIS D 68 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TRP E 37 " --> pdb=" O ILE E 44 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AB8, first strand: chain 'E' and resid 15 through 19 Processing sheet with id=AB9, first strand: chain 'H' and resid 46 through 47 removed outlier: 6.568A pdb=" N GLY H 26 " --> pdb=" O PHE H 33 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG H 35 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA H 24 " --> pdb=" O ARG H 35 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP H 37 " --> pdb=" O PHE H 22 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE H 22 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR H 94 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR H 118 " --> pdb=" O THR H 94 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN H 96 " --> pdb=" O TYR H 116 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N TYR H 116 " --> pdb=" O GLN H 96 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N MET H 98 " --> pdb=" O HIS H 114 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS H 114 " --> pdb=" O MET H 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY H 100 " --> pdb=" O GLY H 112 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY H 112 " --> pdb=" O GLY H 100 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP H 102 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS H 114 " --> pdb=" O ALA H 125 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA H 125 " --> pdb=" O HIS H 114 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR H 116 " --> pdb=" O TYR H 123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 189 through 192 removed outlier: 5.757A pdb=" N PHE H 241 " --> pdb=" O SER H 207 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 189 through 192 removed outlier: 5.757A pdb=" N PHE H 241 " --> pdb=" O SER H 207 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 222 through 223 Processing sheet with id=AC4, first strand: chain 'L' and resid 6 through 11 removed outlier: 5.814A pdb=" N PHE L 62 " --> pdb=" O GLY L 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 6 through 11 removed outlier: 5.814A pdb=" N PHE L 62 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER L 55 " --> pdb=" O TYR L 63 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 44 through 45 Processing sheet with id=AC7, first strand: chain 'e' and resid 17 through 19 612 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 4.59 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: 2886 1.33 - 1.45: 2565 1.45 - 1.58: 6243 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 11778 Sorted by residual: bond pdb=" N ILE C 40 " pdb=" CA ILE C 40 " ideal model delta sigma weight residual 1.459 1.490 -0.032 9.10e-03 1.21e+04 1.21e+01 bond pdb=" N GLN C 15 " pdb=" CA GLN C 15 " ideal model delta sigma weight residual 1.454 1.493 -0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" N VAL A 132 " pdb=" CA VAL A 132 " ideal model delta sigma weight residual 1.458 1.497 -0.038 1.20e-02 6.94e+03 1.03e+01 bond pdb=" N GLN e 70 " pdb=" CA GLN e 70 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.18e-02 7.18e+03 9.68e+00 bond pdb=" N ILE e 118 " pdb=" CA ILE e 118 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.18e-02 7.18e+03 8.87e+00 ... (remaining 11773 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.77: 330 106.77 - 113.73: 6487 113.73 - 120.69: 4876 120.69 - 127.65: 4175 127.65 - 134.61: 121 Bond angle restraints: 15989 Sorted by residual: angle pdb=" N ILE C 40 " pdb=" CA ILE C 40 " pdb=" C ILE C 40 " ideal model delta sigma weight residual 113.47 108.91 4.56 1.01e+00 9.80e-01 2.03e+01 angle pdb=" CA GLY B 107 " pdb=" C GLY B 107 " pdb=" O GLY B 107 " ideal model delta sigma weight residual 122.57 118.56 4.01 9.20e-01 1.18e+00 1.90e+01 angle pdb=" N LEU Z 6 " pdb=" CA LEU Z 6 " pdb=" C LEU Z 6 " ideal model delta sigma weight residual 112.88 107.35 5.53 1.29e+00 6.01e-01 1.84e+01 angle pdb=" C TYR H 113 " pdb=" CA TYR H 113 " pdb=" CB TYR H 113 " ideal model delta sigma weight residual 109.70 101.97 7.73 1.81e+00 3.05e-01 1.82e+01 angle pdb=" N GLY e 120 " pdb=" CA GLY e 120 " pdb=" C GLY e 120 " ideal model delta sigma weight residual 112.50 107.62 4.88 1.16e+00 7.43e-01 1.77e+01 ... (remaining 15984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 6443 17.84 - 35.69: 423 35.69 - 53.53: 88 53.53 - 71.38: 14 71.38 - 89.22: 8 Dihedral angle restraints: 6976 sinusoidal: 2773 harmonic: 4203 Sorted by residual: dihedral pdb=" CB CYS E 97 " pdb=" SG CYS E 97 " pdb=" SG CYS E 100 " pdb=" CB CYS E 100 " ideal model delta sinusoidal sigma weight residual 93.00 148.70 -55.70 1 1.00e+01 1.00e-02 4.19e+01 dihedral pdb=" CB CYS A 24 " pdb=" SG CYS A 24 " pdb=" SG CYS A 90 " pdb=" CB CYS A 90 " ideal model delta sinusoidal sigma weight residual 93.00 43.16 49.84 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CA VAL E 96 " pdb=" C VAL E 96 " pdb=" N CYS E 97 " pdb=" CA CYS E 97 " ideal model delta harmonic sigma weight residual -180.00 -153.77 -26.23 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 6973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1260 0.046 - 0.092: 352 0.092 - 0.138: 132 0.138 - 0.185: 21 0.185 - 0.231: 9 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CA VAL C 11 " pdb=" N VAL C 11 " pdb=" C VAL C 11 " pdb=" CB VAL C 11 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ILE D 49 " pdb=" N ILE D 49 " pdb=" C ILE D 49 " pdb=" CB ILE D 49 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA LEU Z 6 " pdb=" N LEU Z 6 " pdb=" C LEU Z 6 " pdb=" CB LEU Z 6 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1771 not shown) Planarity restraints: 2051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU e 69 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C GLU e 69 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU e 69 " 0.021 2.00e-02 2.50e+03 pdb=" N GLN e 70 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 233 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C ILE B 233 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE B 233 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 234 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 111 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C THR B 111 " -0.038 2.00e-02 2.50e+03 pdb=" O THR B 111 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL B 112 " 0.013 2.00e-02 2.50e+03 ... (remaining 2048 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 5261 2.96 - 3.45: 10926 3.45 - 3.93: 19387 3.93 - 4.42: 22068 4.42 - 4.90: 37405 Nonbonded interactions: 95047 Sorted by model distance: nonbonded pdb=" O SER B 170 " pdb=" OG SER B 170 " model vdw 2.475 2.440 nonbonded pdb=" O5 NAG A 303 " pdb=" O6 NAG A 303 " model vdw 2.488 2.432 nonbonded pdb=" O ASP A 129 " pdb=" OD1 ASP A 129 " model vdw 2.508 3.040 nonbonded pdb=" O5 NAG A 301 " pdb=" O6 NAG A 301 " model vdw 2.538 2.432 nonbonded pdb=" N ASP D 10 " pdb=" OD1 ASP D 10 " model vdw 2.540 2.520 ... (remaining 95042 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 'E' and (resid 11 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 133)) selection = (chain 'e' and (resid 11 through 47 or (resid 48 through 49 and (name N or name \ CA or name C or name O or name CB )) or resid 50 or (resid 51 and (name N or nam \ e CA or name C or name O or name CB )) or resid 52 through 81 or (resid 82 and ( \ name N or name CA or name C or name O or name CB )) or resid 83 through 132 or ( \ resid 133 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'Z' and (resid 6 through 33 or (resid 34 and (name N or name CA or name C \ or name O or name CB )))) selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.040 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: 12.950 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 31.730 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 11778 Z= 0.370 Angle : 0.774 7.730 15989 Z= 0.511 Chirality : 0.051 0.231 1774 Planarity : 0.004 0.035 2045 Dihedral : 12.626 89.220 4225 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: -0.08 (0.22), residues: 1421 helix: 2.15 (0.27), residues: 342 sheet: -0.27 (0.25), residues: 415 loop : -1.08 (0.22), residues: 664 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.396 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.2899 time to fit residues: 63.0198 Evaluate side-chains 133 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 125 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 113 GLN A 189 ASN B 212 GLN E 38 GLN e 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 11778 Z= 0.283 Angle : 0.506 5.463 15989 Z= 0.269 Chirality : 0.042 0.151 1774 Planarity : 0.004 0.043 2045 Dihedral : 4.197 29.019 1575 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.30 (0.22), residues: 1421 helix: 2.63 (0.27), residues: 343 sheet: -0.07 (0.25), residues: 414 loop : -0.93 (0.22), residues: 664 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.380 Fit side-chains outliers start: 18 outliers final: 17 residues processed: 160 average time/residue: 0.2654 time to fit residues: 59.7413 Evaluate side-chains 159 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1018 time to fit residues: 5.1989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 113 GLN A 189 ASN L 24 ASN ** L 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 11778 Z= 0.284 Angle : 0.494 5.312 15989 Z= 0.262 Chirality : 0.042 0.223 1774 Planarity : 0.004 0.046 2045 Dihedral : 4.232 29.513 1575 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.40 (0.22), residues: 1421 helix: 2.67 (0.26), residues: 343 sheet: 0.05 (0.26), residues: 411 loop : -0.88 (0.22), residues: 667 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 1.348 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 153 average time/residue: 0.2756 time to fit residues: 58.6684 Evaluate side-chains 145 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 1.365 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1315 time to fit residues: 3.0183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 65 optimal weight: 0.0050 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 133 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 111 optimal weight: 6.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 113 GLN A 189 ASN L 8 GLN L 84 HIS e 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 11778 Z= 0.174 Angle : 0.439 4.936 15989 Z= 0.235 Chirality : 0.040 0.145 1774 Planarity : 0.003 0.034 2045 Dihedral : 3.968 30.034 1575 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.22), residues: 1421 helix: 2.89 (0.26), residues: 343 sheet: 0.19 (0.26), residues: 412 loop : -0.80 (0.22), residues: 666 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.416 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 147 average time/residue: 0.2476 time to fit residues: 52.6170 Evaluate side-chains 147 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 139 time to evaluate : 1.443 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1482 time to fit residues: 3.8345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 7.9990 chunk 1 optimal weight: 0.0670 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 113 optimal weight: 0.0470 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 119 optimal weight: 0.0970 chunk 33 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 113 GLN B 83 GLN B 102 GLN e 39 HIS e 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 11778 Z= 0.153 Angle : 0.430 4.923 15989 Z= 0.229 Chirality : 0.040 0.178 1774 Planarity : 0.003 0.036 2045 Dihedral : 3.886 30.978 1575 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.82 (0.22), residues: 1421 helix: 3.01 (0.26), residues: 344 sheet: 0.31 (0.26), residues: 423 loop : -0.64 (0.23), residues: 654 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 1.297 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 153 average time/residue: 0.2662 time to fit residues: 57.4318 Evaluate side-chains 149 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 1.358 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1269 time to fit residues: 3.8340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 0.0050 chunk 133 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN A 113 GLN A 189 ASN B 83 GLN B 102 GLN e 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.093 11778 Z= 0.426 Angle : 0.557 6.384 15989 Z= 0.292 Chirality : 0.045 0.238 1774 Planarity : 0.004 0.048 2045 Dihedral : 4.376 30.402 1575 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.47 (0.22), residues: 1421 helix: 2.61 (0.26), residues: 343 sheet: 0.13 (0.25), residues: 412 loop : -0.80 (0.23), residues: 666 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 1.377 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 155 average time/residue: 0.2632 time to fit residues: 57.6873 Evaluate side-chains 152 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 141 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1036 time to fit residues: 3.8334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 189 ASN e 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 11778 Z= 0.266 Angle : 0.484 5.279 15989 Z= 0.255 Chirality : 0.042 0.184 1774 Planarity : 0.004 0.038 2045 Dihedral : 4.207 30.668 1575 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.54 (0.22), residues: 1421 helix: 2.77 (0.26), residues: 343 sheet: 0.13 (0.26), residues: 411 loop : -0.78 (0.23), residues: 667 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 1.258 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 144 average time/residue: 0.2635 time to fit residues: 53.9572 Evaluate side-chains 143 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 138 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1227 time to fit residues: 2.9756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 0.0570 chunk 65 optimal weight: 0.7980 chunk 12 optimal weight: 0.0170 chunk 104 optimal weight: 20.0000 chunk 120 optimal weight: 1.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 189 ASN e 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 11778 Z= 0.159 Angle : 0.437 4.912 15989 Z= 0.232 Chirality : 0.040 0.146 1774 Planarity : 0.003 0.039 2045 Dihedral : 3.955 31.374 1575 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.75 (0.22), residues: 1421 helix: 2.99 (0.26), residues: 345 sheet: 0.19 (0.26), residues: 427 loop : -0.66 (0.23), residues: 649 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 1.259 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 152 average time/residue: 0.2652 time to fit residues: 56.6929 Evaluate side-chains 145 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1752 time to fit residues: 3.3263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.0060 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 189 ASN B 83 GLN e 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 11778 Z= 0.213 Angle : 0.462 5.800 15989 Z= 0.243 Chirality : 0.041 0.152 1774 Planarity : 0.003 0.043 2045 Dihedral : 4.021 31.637 1575 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1421 helix: 2.96 (0.26), residues: 345 sheet: 0.27 (0.26), residues: 418 loop : -0.68 (0.23), residues: 658 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 1.348 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 150 average time/residue: 0.2632 time to fit residues: 55.7521 Evaluate side-chains 153 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 1.312 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1160 time to fit residues: 3.5187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 189 ASN B 83 GLN e 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 11778 Z= 0.306 Angle : 0.508 7.188 15989 Z= 0.266 Chirality : 0.042 0.172 1774 Planarity : 0.004 0.067 2045 Dihedral : 4.227 31.694 1575 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.61 (0.22), residues: 1421 helix: 2.80 (0.26), residues: 345 sheet: 0.18 (0.25), residues: 417 loop : -0.74 (0.23), residues: 659 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 145 time to evaluate : 1.376 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 147 average time/residue: 0.2761 time to fit residues: 56.8632 Evaluate side-chains 143 residues out of total 1267 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.346 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.0370 chunk 109 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 112 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN A 189 ASN e 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.183837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.151659 restraints weight = 12256.684| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.46 r_work: 0.3261 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11778 Z= 0.172 Angle : 0.445 6.723 15989 Z= 0.235 Chirality : 0.040 0.141 1774 Planarity : 0.003 0.046 2045 Dihedral : 3.962 31.546 1575 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % 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: 0.82 (0.22), residues: 1421 helix: 3.04 (0.26), residues: 345 sheet: 0.33 (0.26), residues: 418 loop : -0.68 (0.23), residues: 658 =============================================================================== Job complete usr+sys time: 2574.93 seconds wall clock time: 47 minutes 35.86 seconds (2855.86 seconds total)