Starting phenix.real_space_refine (version: dev) on Thu May 12 22:35:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/05_2022/6dw1_8923_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/05_2022/6dw1_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_8923/05_2022/6dw1_8923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/05_2022/6dw1_8923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/05_2022/6dw1_8923_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/05_2022/6dw1_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 Convert atoms to be neutral 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-4597/modules/chem_data/mon_lib" Total number of atoms: 8595 Number of models: 1 Model: "" Number of chains: 9 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: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {'ABU': 1, 'BMA': 1, 'NAG': 2, 'MAN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 97 Unusual residues: {'ABU': 2, 'BMA': 1, 'NAG': 2, 'MAN': 4} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.49, per 1000 atoms: 0.64 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 A 404 " - " MAN A 405 " ALPHA1-3 " BMA A 403 " - " MAN A 404 " " MAN A 406 " - " MAN A 407 " " BMA C 403 " - " MAN C 404 " ALPHA1-6 " BMA A 403 " - " MAN A 406 " BETA1-4 " NAG A 401 " - " NAG A 402 " " NAG A 402 " - " BMA A 403 " " NAG B 501 " - " NAG B 502 " " NAG B 502 " - " BMA B 503 " " NAG B 504 " - " NAG B 505 " " NAG C 401 " - " NAG C 402 " " NAG C 402 " - " BMA C 403 " " NAG E 501 " - " NAG E 502 " " NAG E 502 " - " BMA E 503 " " NAG E 504 " - " NAG E 505 " NAG-ASN " NAG A 401 " - " ASN A 110 " " NAG B 501 " - " ASN B 149 " " NAG B 504 " - " ASN B 80 " " NAG C 401 " - " ASN C 110 " " NAG E 501 " - " ASN E 149 " " NAG E 504 " - " ASN E 80 " Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.3 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: 0.79 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: 2.01 Time building geometry restraints manager: 3.97 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 E 505 " pdb=" C3 NAG E 505 " pdb=" C4 NAG E 505 " pdb=" C5 NAG E 505 " 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 E 501 " pdb=" C2 NAG E 501 " pdb=" C3 NAG E 501 " pdb=" C4 NAG E 501 " 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 E 502 " pdb=" C2 NAG E 502 " pdb=" C3 NAG E 502 " pdb=" C4 NAG E 502 " 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 C 401 " pdb=" ND2 ASN C 110 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " 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 A 406 " pdb=" O6 BMA A 403 " pdb=" C2 MAN A 406 " pdb=" O5 MAN A 406 " 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 C 402 " pdb=" O4 NAG C 401 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " 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 401 through 404)) 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 401 through 404)) } 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 )) or resid 501 through 50 \ 5)) 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 or resid 501 through 505)) } 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: 4.300 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: 23.020 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.080 Process input model: 27.660 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.450 ------------------------------------------------------------------------------- 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= 0.352 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 : 4.79 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 : 1.017 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: 0.2512 time to fit residues: 91.3964 Evaluate side-chains 168 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3612 ------------------------------------------------------------------------------- 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: 4.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 0.0470 chunk 93 optimal weight: 3.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN B 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 8783 Z= 0.354 Angle : 0.701 9.315 11922 Z= 0.362 Chirality : 0.048 0.292 1403 Planarity : 0.005 0.059 1483 Dihedral : 11.377 103.161 1334 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % 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: -3.06 (0.24), residues: 1036 helix: -3.53 (0.36), residues: 71 sheet: -1.75 (0.23), residues: 403 loop : -2.01 (0.25), residues: 562 *********************** 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 199 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 168 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 19 residues processed: 193 average time/residue: 0.1962 time to fit residues: 52.6916 Evaluate side-chains 171 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0952 time to fit residues: 4.4646 ------------------------------------------------------------------------------- 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: 4.9990 chunk 29 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 0.0070 chunk 101 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 195 GLN E 64 GLN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 8783 Z= 0.246 Angle : 0.617 8.385 11922 Z= 0.318 Chirality : 0.045 0.278 1403 Planarity : 0.004 0.053 1483 Dihedral : 11.199 103.159 1334 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 2.35 % 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: -2.59 (0.25), residues: 1036 helix: -2.56 (0.55), residues: 64 sheet: -1.48 (0.24), residues: 405 loop : -1.76 (0.25), residues: 567 *********************** 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 188 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 176 average time/residue: 0.1969 time to fit residues: 48.3756 Evaluate side-chains 170 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0924 time to fit residues: 3.6032 ------------------------------------------------------------------------------- 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: 3.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 0.0570 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 101 HIS A 195 GLN E 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 8783 Z= 0.254 Angle : 0.625 11.212 11922 Z= 0.316 Chirality : 0.045 0.264 1403 Planarity : 0.004 0.058 1483 Dihedral : 11.130 103.413 1334 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 2.12 % 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: -2.32 (0.25), residues: 1036 helix: -2.11 (0.60), residues: 64 sheet: -1.35 (0.24), residues: 400 loop : -1.57 (0.26), residues: 572 *********************** 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 179 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 15 residues processed: 168 average time/residue: 0.2025 time to fit residues: 47.3570 Evaluate side-chains 169 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1062 time to fit residues: 4.0609 ------------------------------------------------------------------------------- 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: 5.9990 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 101 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.069 8783 Z= 0.616 Angle : 0.796 10.868 11922 Z= 0.408 Chirality : 0.052 0.288 1403 Planarity : 0.006 0.073 1483 Dihedral : 11.611 104.845 1334 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.85 % Favored : 93.05 % Rotamer Outliers : 2.46 % 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: -2.45 (0.24), residues: 1036 helix: -2.02 (0.61), residues: 64 sheet: -1.31 (0.24), residues: 403 loop : -1.79 (0.24), residues: 569 *********************** 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 167 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.093 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 159 average time/residue: 0.1882 time to fit residues: 42.1878 Evaluate side-chains 154 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0852 time to fit residues: 3.2562 ------------------------------------------------------------------------------- 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: 9.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 101 HIS ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8783 Z= 0.197 Angle : 0.611 9.373 11922 Z= 0.312 Chirality : 0.045 0.279 1403 Planarity : 0.004 0.060 1483 Dihedral : 11.242 103.492 1334 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % 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: -2.10 (0.25), residues: 1036 helix: -1.69 (0.64), residues: 64 sheet: -1.11 (0.25), residues: 399 loop : -1.54 (0.26), residues: 573 *********************** 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 173 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 0.990 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 170 average time/residue: 0.2066 time to fit residues: 48.8511 Evaluate side-chains 155 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0959 time to fit residues: 2.2214 ------------------------------------------------------------------------------- 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: 5.9990 chunk 56 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 chunk 60 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 101 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8783 Z= 0.189 Angle : 0.605 11.592 11922 Z= 0.306 Chirality : 0.044 0.265 1403 Planarity : 0.004 0.060 1483 Dihedral : 11.119 103.829 1334 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer Outliers : 1.45 % 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: -1.93 (0.26), residues: 1036 helix: -1.46 (0.67), residues: 64 sheet: -1.02 (0.24), residues: 401 loop : -1.41 (0.26), residues: 571 *********************** 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 167 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 1.045 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 161 average time/residue: 0.1971 time to fit residues: 44.6442 Evaluate side-chains 153 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 1.079 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0897 time to fit residues: 2.5092 ------------------------------------------------------------------------------- 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: 6.9990 chunk 59 optimal weight: 0.0170 chunk 29 optimal weight: 6.9990 chunk 19 optimal weight: 0.1980 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 8.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 101 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3762 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= 0.205 Angle : 0.607 10.677 11922 Z= 0.307 Chirality : 0.044 0.255 1403 Planarity : 0.004 0.060 1483 Dihedral : 11.062 103.851 1334 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 1.12 % 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: -1.83 (0.26), residues: 1036 helix: -1.52 (0.66), residues: 64 sheet: -0.99 (0.24), residues: 410 loop : -1.28 (0.27), residues: 562 *********************** 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 164 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 1.141 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 159 average time/residue: 0.1975 time to fit residues: 44.1810 Evaluate side-chains 156 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0919 time to fit residues: 2.6529 ------------------------------------------------------------------------------- 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: 10.0000 chunk 92 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 0.0770 chunk 87 optimal weight: 5.9990 chunk 60 optimal weight: 0.0870 chunk 97 optimal weight: 6.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 80 GLN C 115 ASN A 101 HIS ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 8783 Z= 0.164 Angle : 0.602 10.092 11922 Z= 0.301 Chirality : 0.044 0.256 1403 Planarity : 0.004 0.059 1483 Dihedral : 10.956 103.680 1334 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 0.67 % 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: -1.74 (0.26), residues: 1036 helix: -1.41 (0.67), residues: 64 sheet: -1.00 (0.24), residues: 418 loop : -1.17 (0.27), residues: 554 *********************** 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: 6 poor density : 153 time to evaluate : 1.096 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 156 average time/residue: 0.2051 time to fit residues: 44.4658 Evaluate side-chains 147 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0809 time to fit residues: 1.5919 ------------------------------------------------------------------------------- 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: 4.9990 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 81 optimal weight: 0.0070 chunk 8 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 101 HIS ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8783 Z= 0.178 Angle : 0.596 10.308 11922 Z= 0.300 Chirality : 0.044 0.250 1403 Planarity : 0.004 0.060 1483 Dihedral : 10.918 103.816 1334 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % 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: -1.68 (0.26), residues: 1036 helix: -1.39 (0.68), residues: 64 sheet: -0.99 (0.24), residues: 424 loop : -1.09 (0.28), residues: 548 ********************** 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 158 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 1.118 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 156 average time/residue: 0.2117 time to fit residues: 45.5927 Evaluate side-chains 146 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1174 time to fit residues: 1.9241 ------------------------------------------------------------------------------- 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: 0.7980 chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 0.0070 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 4 optimal weight: 0.0370 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.109985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095584 restraints weight = 16799.195| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.48 r_work: 0.3378 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work: 0.3358 rms_B_bonded: 2.28 restraints_weight: 0.1250 r_work: 0.3347 rms_B_bonded: 2.37 restraints_weight: 0.0625 r_work: 0.3335 rms_B_bonded: 2.49 restraints_weight: 0.0312 r_work: 0.3323 rms_B_bonded: 2.65 restraints_weight: 0.0156 r_work: 0.3310 rms_B_bonded: 2.84 restraints_weight: 0.0078 r_work: 0.3296 rms_B_bonded: 3.06 restraints_weight: 0.0039 r_work: 0.3281 rms_B_bonded: 3.33 restraints_weight: 0.0020 r_work: 0.3265 rms_B_bonded: 3.63 restraints_weight: 0.0010 r_work: 0.3247 rms_B_bonded: 3.98 restraints_weight: 0.0005 r_work: 0.3228 rms_B_bonded: 4.38 restraints_weight: 0.0002 r_work: 0.3207 rms_B_bonded: 4.83 restraints_weight: 0.0001 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 8783 Z= 0.162 Angle : 0.583 10.174 11922 Z= 0.293 Chirality : 0.043 0.249 1403 Planarity : 0.004 0.058 1483 Dihedral : 10.860 103.693 1334 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % 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: -1.57 (0.26), residues: 1036 helix: -1.75 (0.64), residues: 70 sheet: -0.88 (0.25), residues: 405 loop : -0.99 (0.27), residues: 561 =============================================================================== Job complete usr+sys time: 2151.11 seconds wall clock time: 39 minutes 38.85 seconds (2378.85 seconds total)