Starting phenix.real_space_refine (version: dev) on Sat Feb 18 18:31:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/02_2023/6dw1_8923_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/02_2023/6dw1_8923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/02_2023/6dw1_8923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/02_2023/6dw1_8923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/02_2023/6dw1_8923_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/02_2023/6dw1_8923_updated.pdb" } resolution = 3.1 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= 1.000 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 Process input model Symmetric amino acids flipped Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 176": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "C ARG 16": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C ARG 172": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "A ARG 16": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 141": "NH1" <-> "NH2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8595 Number of models: 1 Model: "" Number of chains: 13 Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1612 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 8, 'TRANS': 199} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1673 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 200} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1665 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 200} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1672 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 198} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1685 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 200} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "K" 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 Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {'ABU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.41, per 1000 atoms: 0.63 Number of scatterers: 8595 At special positions: 0 Unit cell: (90.86, 95.403, 86.966, 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 45 16.00 O 1646 8.00 N 1443 7.00 C 5461 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 151 " - pdb=" SG CYS D 165 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " 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 ALPHA1-2 " MAN G 4 " - " MAN G 5 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " MAN G 6 " - " MAN G 7 " ALPHA1-6 " BMA G 3 " - " MAN G 6 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG F 1 " - " ASN C 110 " " NAG G 1 " - " ASN A 110 " " NAG H 1 " - " ASN E 149 " " NAG I 1 " - " ASN E 80 " " NAG J 1 " - " ASN B 149 " " NAG K 1 " - " ASN B 80 " Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 1.2 seconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 15 helices and 17 sheets defined 7.2% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'D' and resid 26 through 32 removed outlier: 3.575A pdb=" N ILE D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.615A pdb=" N ASP A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 87 through 90 No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'E' and resid 11 through 19 removed outlier: 3.556A pdb=" N THR E 15 " --> pdb=" O TYR E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 171 through 174 removed outlier: 3.670A pdb=" N ALA E 174 " --> pdb=" O GLY E 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 174' Processing helix chain 'B' and resid 9 through 20 removed outlier: 3.555A pdb=" N GLU B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing sheet with id= A, first strand: chain 'D' and resid 180 through 183 removed outlier: 6.863A pdb=" N LEU D 52 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR D 83 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP D 75 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE D 62 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR D 72 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG D 138 " --> pdb=" O TRP D 134 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 131 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 166 through 169 removed outlier: 3.597A pdb=" N ARG D 207 " --> pdb=" O TYR D 226 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY D 205 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N SER D 230 " --> pdb=" O PHE D 203 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N PHE D 203 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 211 through 214 Processing sheet with id= D, first strand: chain 'C' and resid 166 through 170 removed outlier: 5.935A pdb=" N THR C 38 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU C 169 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL C 40 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASP C 62 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE C 49 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C 60 " --> pdb=" O PHE C 49 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 82 through 85 removed outlier: 4.265A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 149 through 157 removed outlier: 3.587A pdb=" N GLY C 194 " --> pdb=" O HIS C 217 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS C 219 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU C 192 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 201 through 203 Processing sheet with id= H, first strand: chain 'A' and resid 166 through 170 removed outlier: 6.588A pdb=" N THR A 38 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLU A 169 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 40 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU A 39 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 70 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP A 69 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 98 through 100 Processing sheet with id= J, first strand: chain 'A' and resid 149 through 153 removed outlier: 3.771A pdb=" N GLY A 194 " --> pdb=" O HIS A 217 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LYS A 219 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LEU A 192 " --> pdb=" O LYS A 219 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 46 through 49 removed outlier: 7.131A pdb=" N ASP A 62 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.736A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASP E 37 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS E 68 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.889A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS E 192 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.823A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.336A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP B 37 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS B 68 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.763A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.843A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 591 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: 2.19 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2705 1.34 - 1.46: 2077 1.46 - 1.58: 3921 1.58 - 1.70: 0 1.70 - 1.81: 80 Bond restraints: 8783 Sorted by residual: bond pdb=" C PHE C 145 " pdb=" N PRO C 146 " ideal model delta sigma weight residual 1.336 1.377 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" CG1 ILE E 164 " pdb=" CD1 ILE E 164 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.44e+00 bond pdb=" C PHE D 158 " pdb=" N PRO D 159 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.50e+00 bond pdb=" C ARG D 43 " pdb=" N PRO D 44 " ideal model delta sigma weight residual 1.334 1.363 -0.030 2.34e-02 1.83e+03 1.60e+00 bond pdb=" C TYR B 143 " pdb=" N PRO B 144 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.23e-02 6.61e+03 1.58e+00 ... (remaining 8778 not shown) Histogram of bond angle deviations from ideal: 98.61 - 105.70: 195 105.70 - 112.78: 4692 112.78 - 119.86: 2810 119.86 - 126.95: 4116 126.95 - 134.03: 109 Bond angle restraints: 11922 Sorted by residual: angle pdb=" N PRO D 127 " pdb=" CA PRO D 127 " pdb=" C PRO D 127 " ideal model delta sigma weight residual 112.47 121.32 -8.85 2.06e+00 2.36e-01 1.84e+01 angle pdb=" C ASP A 144 " pdb=" N PHE A 145 " pdb=" CA PHE A 145 " ideal model delta sigma weight residual 120.58 126.06 -5.48 1.32e+00 5.74e-01 1.72e+01 angle pdb=" C ILE E 47 " pdb=" N ASP E 48 " pdb=" CA ASP E 48 " ideal model delta sigma weight residual 121.19 127.49 -6.30 1.59e+00 3.96e-01 1.57e+01 angle pdb=" CA LEU E 145 " pdb=" CB LEU E 145 " pdb=" CG LEU E 145 " ideal model delta sigma weight residual 116.30 130.07 -13.77 3.50e+00 8.16e-02 1.55e+01 angle pdb=" N ASP E 48 " pdb=" CA ASP E 48 " pdb=" C ASP E 48 " ideal model delta sigma weight residual 111.37 117.59 -6.22 1.64e+00 3.72e-01 1.44e+01 ... (remaining 11917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.28: 5066 20.28 - 40.55: 147 40.55 - 60.83: 17 60.83 - 81.11: 6 81.11 - 101.39: 9 Dihedral angle restraints: 5245 sinusoidal: 2184 harmonic: 3061 Sorted by residual: dihedral pdb=" C2 NAG I 2 " pdb=" C3 NAG I 2 " pdb=" C4 NAG I 2 " pdb=" C5 NAG I 2 " ideal model delta sinusoidal sigma weight residual 50.00 -51.39 101.39 1 2.00e+01 2.50e-03 2.87e+01 dihedral pdb=" C1 NAG H 1 " pdb=" C2 NAG H 1 " pdb=" C3 NAG H 1 " pdb=" C4 NAG H 1 " ideal model delta sinusoidal sigma weight residual -50.00 50.17 -100.17 1 2.00e+01 2.50e-03 2.82e+01 dihedral pdb=" C1 NAG H 2 " pdb=" C2 NAG H 2 " pdb=" C3 NAG H 2 " pdb=" C4 NAG H 2 " ideal model delta sinusoidal sigma weight residual -50.00 48.04 -98.04 1 2.00e+01 2.50e-03 2.74e+01 ... (remaining 5242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1238 0.080 - 0.160: 151 0.160 - 0.241: 12 0.241 - 0.321: 1 0.321 - 0.401: 1 Chirality restraints: 1403 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 110 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C1 MAN G 6 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 6 " pdb=" O5 MAN G 6 " both_signs ideal model delta sigma weight residual False 2.40 2.36 0.04 2.00e-02 2.50e+03 3.08e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 1.75e+00 ... (remaining 1400 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 143 " -0.050 5.00e-02 4.00e+02 7.46e-02 8.89e+00 pdb=" N PRO E 144 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO E 144 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 144 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 49 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO D 50 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 50 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 50 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 145 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO A 146 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.032 5.00e-02 4.00e+02 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2537 2.82 - 3.34: 7015 3.34 - 3.86: 14325 3.86 - 4.38: 16191 4.38 - 4.90: 28649 Nonbonded interactions: 68717 Sorted by model distance: nonbonded pdb=" OG1 THR A 98 " pdb=" OH TYR A 168 " model vdw 2.304 2.440 nonbonded pdb=" OH TYR B 57 " pdb=" O THR B 151 " model vdw 2.315 2.440 nonbonded pdb=" NH1 ARG D 129 " pdb=" OH TYR D 141 " model vdw 2.334 2.520 nonbonded pdb=" OG SER B 46 " pdb=" OD1 ASP B 48 " model vdw 2.343 2.440 nonbonded pdb=" OD1 ASP E 146 " pdb=" NH1 ARG E 216 " model vdw 2.351 2.520 ... (remaining 68712 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 12 through 70 or (resid 71 through 72 and (name N or name \ CA or name C or name O or name CB )) or resid 73 through 76 or (resid 77 and (na \ me N or name CA or name C or name O or name CB )) or resid 78 through 79 or (res \ id 80 and (name N or name CA or name C or name O or name CB )) or resid 81 throu \ gh 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or \ resid 138 through 221 or resid 408)) selection = (chain 'C' and (resid 12 through 34 or (resid 35 through 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 54 or (resid 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 86 or (res \ id 87 and (name N or name CA or name C or name O or name CB )) or resid 88 throu \ gh 172 or (resid 173 and (name N or name CA or name C or name O or name CB )) or \ resid 174 through 221 or resid 405)) } ncs_group { reference = (chain 'B' and (resid 10 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 191 or (resid 192 and (name N or n \ ame CA or name C or name O or name CB )) or resid 193 through 216 or (resid 217 \ and (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 10 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 29 or (resid 30 and (name N or nam \ e CA or name C or name O or name CB )) or resid 31 through 51 or (resid 52 and ( \ name N or name CA or name C or name O or name CB )) or resid 53 through 138 or ( \ resid 139 and (name N or name CA or name C or name O or name CB )) or resid 140 \ through 217)) } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' } 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 5461 2.51 5 N 1443 2.21 5 O 1646 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 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: 7.510 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: 0.000 Extract box with map and model: 25.490 Check model and map are aligned: 0.130 Process input model: 26.620 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.080 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 63.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 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 : 0.005 0.072 8783 Z= 0.351 Angle : 0.906 13.768 11922 Z= 0.475 Chirality : 0.054 0.401 1403 Planarity : 0.006 0.075 1483 Dihedral : 11.315 101.386 3262 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.22), residues: 1036 helix: -4.69 (0.23), residues: 62 sheet: -2.08 (0.24), residues: 371 loop : -2.49 (0.21), residues: 603 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2632 time to fit residues: 95.2944 Evaluate side-chains 169 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.0470 chunk 93 optimal weight: 0.8980 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN A 101 HIS ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 113 ASN E 148 GLN B 54 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 8783 Z= 0.276 Angle : 0.666 9.030 11922 Z= 0.343 Chirality : 0.046 0.291 1403 Planarity : 0.005 0.056 1483 Dihedral : 11.310 102.911 1334 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 3.46 % 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: -3.04 (0.24), residues: 1036 helix: -3.48 (0.36), residues: 69 sheet: -1.70 (0.24), residues: 394 loop : -2.05 (0.24), residues: 573 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 19 residues processed: 196 average time/residue: 0.2063 time to fit residues: 55.5733 Evaluate side-chains 171 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0987 time to fit residues: 4.4113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN E 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8783 Z= 0.198 Angle : 0.608 8.604 11922 Z= 0.312 Chirality : 0.045 0.270 1403 Planarity : 0.004 0.051 1483 Dihedral : 11.112 102.916 1334 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 1.56 % 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: -2.64 (0.25), residues: 1036 helix: -2.64 (0.54), residues: 64 sheet: -1.55 (0.24), residues: 401 loop : -1.76 (0.25), residues: 571 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 173 average time/residue: 0.2073 time to fit residues: 50.0436 Evaluate side-chains 161 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1100 time to fit residues: 3.7277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.0000 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8783 Z= 0.218 Angle : 0.614 10.513 11922 Z= 0.308 Chirality : 0.045 0.256 1403 Planarity : 0.004 0.051 1483 Dihedral : 11.032 103.219 1334 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 1.90 % 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: -2.36 (0.25), residues: 1036 helix: -2.10 (0.62), residues: 63 sheet: -1.42 (0.23), residues: 432 loop : -1.54 (0.27), residues: 541 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 166 average time/residue: 0.2111 time to fit residues: 48.6392 Evaluate side-chains 159 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1137 time to fit residues: 3.2232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 8783 Z= 0.364 Angle : 0.657 10.660 11922 Z= 0.336 Chirality : 0.047 0.264 1403 Planarity : 0.005 0.059 1483 Dihedral : 11.205 103.953 1334 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 2.57 % 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: -2.26 (0.25), residues: 1036 helix: -1.80 (0.63), residues: 64 sheet: -1.27 (0.24), residues: 417 loop : -1.60 (0.26), residues: 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 167 average time/residue: 0.1999 time to fit residues: 46.9816 Evaluate side-chains 157 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0906 time to fit residues: 3.8215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 10.0000 chunk 89 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8783 Z= 0.173 Angle : 0.594 9.395 11922 Z= 0.300 Chirality : 0.044 0.260 1403 Planarity : 0.004 0.056 1483 Dihedral : 11.022 103.428 1334 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 1.34 % 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: -2.00 (0.25), residues: 1036 helix: -1.65 (0.65), residues: 64 sheet: -1.14 (0.24), residues: 401 loop : -1.37 (0.26), residues: 571 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 1.051 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 164 average time/residue: 0.1930 time to fit residues: 44.2410 Evaluate side-chains 157 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 151 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0814 time to fit residues: 2.3070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8783 Z= 0.210 Angle : 0.588 9.761 11922 Z= 0.298 Chirality : 0.044 0.253 1403 Planarity : 0.004 0.057 1483 Dihedral : 10.978 103.747 1334 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.56 % 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: -1.86 (0.26), residues: 1036 helix: -1.42 (0.67), residues: 64 sheet: -1.03 (0.24), residues: 407 loop : -1.31 (0.27), residues: 565 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 0.997 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 155 average time/residue: 0.2058 time to fit residues: 44.8097 Evaluate side-chains 150 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 1.438 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1055 time to fit residues: 2.3167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 8783 Z= 0.396 Angle : 0.684 11.279 11922 Z= 0.348 Chirality : 0.047 0.261 1403 Planarity : 0.005 0.063 1483 Dihedral : 11.208 104.480 1334 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 0.89 % 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: -1.91 (0.25), residues: 1036 helix: -1.29 (0.68), residues: 64 sheet: -1.07 (0.24), residues: 408 loop : -1.36 (0.26), residues: 564 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 1.086 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 149 average time/residue: 0.2050 time to fit residues: 42.5682 Evaluate side-chains 146 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0892 time to fit residues: 2.6738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.0970 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 80 GLN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8783 Z= 0.184 Angle : 0.601 10.066 11922 Z= 0.304 Chirality : 0.044 0.254 1403 Planarity : 0.004 0.056 1483 Dihedral : 11.033 103.682 1334 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 0.89 % 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: -1.69 (0.26), residues: 1036 helix: -1.22 (0.68), residues: 64 sheet: -0.93 (0.25), residues: 404 loop : -1.20 (0.26), residues: 568 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 151 time to evaluate : 1.106 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 156 average time/residue: 0.2084 time to fit residues: 45.2007 Evaluate side-chains 148 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 145 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0838 time to fit residues: 1.9490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 8783 Z= 0.218 Angle : 0.614 11.139 11922 Z= 0.310 Chirality : 0.044 0.253 1403 Planarity : 0.004 0.057 1483 Dihedral : 10.990 103.958 1334 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.45 % 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: -1.65 (0.26), residues: 1036 helix: -1.40 (0.67), residues: 64 sheet: -0.88 (0.25), residues: 404 loop : -1.17 (0.27), residues: 568 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 1.089 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 151 average time/residue: 0.2030 time to fit residues: 43.4805 Evaluate side-chains 152 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 149 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0908 time to fit residues: 1.9343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 0.0010 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN A 195 GLN E 90 GLN B 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094760 restraints weight = 16911.386| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.46 r_work: 0.3278 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8783 Z= 0.173 Angle : 0.596 11.127 11922 Z= 0.301 Chirality : 0.043 0.249 1403 Planarity : 0.004 0.055 1483 Dihedral : 10.905 103.737 1334 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer Outliers : 0.34 % 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: -1.52 (0.26), residues: 1036 helix: -1.34 (0.68), residues: 64 sheet: -0.78 (0.25), residues: 404 loop : -1.08 (0.27), residues: 568 =============================================================================== Job complete usr+sys time: 2297.82 seconds wall clock time: 42 minutes 27.23 seconds (2547.23 seconds total)