Starting phenix.real_space_refine on Wed Feb 14 04:31:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/02_2024/6dw1_8923_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/02_2024/6dw1_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_2024/6dw1_8923.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/02_2024/6dw1_8923.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/02_2024/6dw1_8923_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dw1_8923/02_2024/6dw1_8923_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 12 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: 21 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: 9 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 dihedrals: 6 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: 9 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 dihedrals: 6 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: 5.16, per 1000 atoms: 0.60 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: 3.55 Conformation dependent library (CDL) restraints added in 1.7 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: 2.00 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: 2.14 Time building geometry restraints manager: 3.81 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=" C3 MAN F 4 " pdb=" C4 MAN F 4 " ideal model delta sigma weight residual 1.524 1.575 -0.051 2.00e-02 2.50e+03 6.42e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.564 -0.045 2.00e-02 2.50e+03 5.00e+00 bond pdb=" C5 MAN G 4 " pdb=" O5 MAN G 4 " ideal model delta sigma weight residual 1.418 1.462 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C1 MAN G 7 " pdb=" O5 MAN G 7 " ideal model delta sigma weight residual 1.399 1.440 -0.041 2.00e-02 2.50e+03 4.22e+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 - 23.27: 5235 23.27 - 46.55: 151 46.55 - 69.82: 37 69.82 - 93.09: 40 93.09 - 116.36: 43 Dihedral angle restraints: 5506 sinusoidal: 2445 harmonic: 3061 Sorted by residual: dihedral pdb=" CA THR D 126 " pdb=" C THR D 126 " pdb=" N PRO D 127 " pdb=" CA PRO D 127 " ideal model delta harmonic sigma weight residual -180.00 -154.77 -25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " pdb=" SG CYS E 150 " pdb=" CB CYS E 150 " ideal model delta sinusoidal sigma weight residual 93.00 50.43 42.57 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" CA THR C 112 " pdb=" C THR C 112 " pdb=" N MET C 113 " pdb=" CA MET C 113 " ideal model delta harmonic sigma weight residual 180.00 155.13 24.87 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 5503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1216 0.080 - 0.160: 168 0.160 - 0.241: 13 0.241 - 0.321: 4 0.321 - 0.401: 2 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=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.60 0.33 2.00e-01 2.50e+01 2.66e+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 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: 5.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 23.010 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.030 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 8783 Z= 0.379 Angle : 0.972 13.768 11922 Z= 0.486 Chirality : 0.058 0.401 1403 Planarity : 0.006 0.075 1483 Dihedral : 18.013 116.363 3523 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 % Allowed : 5.36 % Favored : 94.64 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 94 HIS 0.011 0.002 HIS A 101 PHE 0.026 0.003 PHE A 99 TYR 0.018 0.002 TYR C 168 ARG 0.011 0.001 ARG C 131 *********************** 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 : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8391 (mttt) cc_final: 0.8014 (tmtt) REVERT: C 113 MET cc_start: 0.8047 (mmm) cc_final: 0.7779 (mmt) REVERT: A 17 ILE cc_start: 0.8896 (tp) cc_final: 0.8544 (mt) REVERT: A 59 TYR cc_start: 0.9130 (p90) cc_final: 0.8882 (p90) REVERT: E 47 ILE cc_start: 0.9070 (mm) cc_final: 0.8677 (mm) REVERT: E 180 LYS cc_start: 0.8996 (mptt) cc_final: 0.8690 (mtpt) REVERT: B 142 ARG cc_start: 0.6989 (pmm-80) cc_final: 0.6661 (ptm160) REVERT: B 160 THR cc_start: 0.8652 (m) cc_final: 0.8448 (p) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.2551 time to fit residues: 92.4666 Evaluate side-chains 172 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.8140 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8783 Z= 0.272 Angle : 0.723 8.705 11922 Z= 0.351 Chirality : 0.048 0.245 1403 Planarity : 0.005 0.056 1483 Dihedral : 16.545 97.617 1595 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.46 % Allowed : 11.06 % Favored : 85.47 % 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: -2.98 (0.24), residues: 1036 helix: -3.41 (0.37), residues: 69 sheet: -1.65 (0.24), residues: 399 loop : -2.01 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 94 HIS 0.007 0.001 HIS C 101 PHE 0.017 0.002 PHE C 64 TYR 0.014 0.002 TYR D 141 ARG 0.006 0.001 ARG B 114 *********************** 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 206 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8374 (mttt) cc_final: 0.8002 (tmtt) REVERT: C 212 MET cc_start: 0.8218 (mmm) cc_final: 0.7455 (mmm) REVERT: A 17 ILE cc_start: 0.8889 (tp) cc_final: 0.8612 (mp) REVERT: A 39 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6927 (mm-30) REVERT: A 59 TYR cc_start: 0.9155 (p90) cc_final: 0.8851 (p90) REVERT: E 47 ILE cc_start: 0.9083 (mm) cc_final: 0.8711 (mm) REVERT: E 103 LYS cc_start: 0.8395 (mtmm) cc_final: 0.8160 (mtmm) REVERT: E 143 TYR cc_start: 0.7733 (t80) cc_final: 0.7026 (m-80) REVERT: B 142 ARG cc_start: 0.7227 (pmm-80) cc_final: 0.6612 (ptm160) REVERT: B 160 THR cc_start: 0.8646 (m) cc_final: 0.8302 (p) outliers start: 31 outliers final: 19 residues processed: 200 average time/residue: 0.2008 time to fit residues: 55.3650 Evaluate side-chains 173 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 152 LEU 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: 2.9990 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN E 64 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8783 Z= 0.265 Angle : 0.671 8.153 11922 Z= 0.328 Chirality : 0.047 0.243 1403 Planarity : 0.004 0.053 1483 Dihedral : 12.437 91.194 1595 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.36 % Allowed : 11.84 % Favored : 83.80 % 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: -2.58 (0.25), residues: 1036 helix: -2.59 (0.52), residues: 71 sheet: -1.46 (0.24), residues: 411 loop : -1.73 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 92 HIS 0.004 0.001 HIS C 101 PHE 0.023 0.002 PHE C 64 TYR 0.015 0.002 TYR E 126 ARG 0.007 0.000 ARG A 163 *********************** 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 208 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8416 (mttt) cc_final: 0.8054 (tmtt) REVERT: C 212 MET cc_start: 0.8199 (mmm) cc_final: 0.7488 (mmm) REVERT: A 17 ILE cc_start: 0.8894 (tp) cc_final: 0.8627 (mp) REVERT: A 27 ASN cc_start: 0.8181 (t0) cc_final: 0.7967 (t0) REVERT: E 47 ILE cc_start: 0.9110 (mm) cc_final: 0.8675 (mm) REVERT: E 143 TYR cc_start: 0.7698 (t80) cc_final: 0.6920 (m-80) REVERT: B 142 ARG cc_start: 0.7509 (pmm-80) cc_final: 0.6933 (ptm160) outliers start: 39 outliers final: 28 residues processed: 193 average time/residue: 0.2031 time to fit residues: 53.9789 Evaluate side-chains 184 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 176 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 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 195 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8783 Z= 0.183 Angle : 0.634 11.280 11922 Z= 0.307 Chirality : 0.045 0.258 1403 Planarity : 0.004 0.050 1483 Dihedral : 10.036 71.532 1595 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.02 % Allowed : 12.74 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.25), residues: 1036 helix: -2.15 (0.57), residues: 71 sheet: -1.29 (0.24), residues: 408 loop : -1.63 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 123 HIS 0.003 0.001 HIS C 101 PHE 0.013 0.001 PHE D 113 TYR 0.012 0.001 TYR E 126 ARG 0.003 0.000 ARG D 97 *********************** 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 197 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 214 LYS cc_start: 0.8405 (mttt) cc_final: 0.8044 (tmtt) REVERT: C 212 MET cc_start: 0.8111 (mmm) cc_final: 0.7449 (mmm) REVERT: A 17 ILE cc_start: 0.8880 (tp) cc_final: 0.8617 (mp) REVERT: E 47 ILE cc_start: 0.9088 (mm) cc_final: 0.8642 (mm) REVERT: E 143 TYR cc_start: 0.7682 (t80) cc_final: 0.6947 (m-80) REVERT: B 142 ARG cc_start: 0.7525 (pmm-80) cc_final: 0.6904 (ptm160) outliers start: 36 outliers final: 28 residues processed: 181 average time/residue: 0.2001 time to fit residues: 50.0792 Evaluate side-chains 178 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 199 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 0.0050 chunk 84 optimal weight: 0.0970 chunk 68 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN A 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8783 Z= 0.207 Angle : 0.617 10.028 11922 Z= 0.302 Chirality : 0.045 0.261 1403 Planarity : 0.004 0.055 1483 Dihedral : 8.712 65.118 1595 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.13 % Allowed : 13.30 % Favored : 82.57 % 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: -2.18 (0.25), residues: 1036 helix: -1.73 (0.65), residues: 64 sheet: -1.20 (0.24), residues: 410 loop : -1.56 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 123 HIS 0.003 0.001 HIS C 101 PHE 0.015 0.001 PHE D 113 TYR 0.015 0.001 TYR A 59 ARG 0.002 0.000 ARG C 172 *********************** 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 197 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 60 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.7185 (t0) REVERT: D 214 LYS cc_start: 0.8427 (mttt) cc_final: 0.8052 (tmtt) REVERT: C 212 MET cc_start: 0.8137 (mmm) cc_final: 0.7474 (mmm) REVERT: A 17 ILE cc_start: 0.8870 (tp) cc_final: 0.8611 (mp) REVERT: E 47 ILE cc_start: 0.9081 (mm) cc_final: 0.8760 (mm) REVERT: E 103 LYS cc_start: 0.8415 (mtmm) cc_final: 0.8191 (mtmm) REVERT: E 143 TYR cc_start: 0.7677 (t80) cc_final: 0.6937 (m-80) REVERT: B 142 ARG cc_start: 0.7586 (pmm-80) cc_final: 0.6981 (ptm160) outliers start: 37 outliers final: 30 residues processed: 182 average time/residue: 0.1947 time to fit residues: 49.1123 Evaluate side-chains 182 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 199 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 99 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8783 Z= 0.161 Angle : 0.603 10.373 11922 Z= 0.293 Chirality : 0.044 0.260 1403 Planarity : 0.004 0.053 1483 Dihedral : 8.008 60.122 1595 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.91 % Allowed : 14.08 % Favored : 82.01 % 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: -1.96 (0.25), residues: 1036 helix: -1.58 (0.67), residues: 64 sheet: -1.10 (0.24), residues: 403 loop : -1.37 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 123 HIS 0.003 0.001 HIS A 150 PHE 0.012 0.001 PHE D 113 TYR 0.020 0.001 TYR E 11 ARG 0.002 0.000 ARG B 207 *********************** 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 199 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 197 ARG cc_start: 0.6141 (OUTLIER) cc_final: 0.5701 (ptt180) REVERT: D 214 LYS cc_start: 0.8411 (mttt) cc_final: 0.8049 (tmtt) REVERT: C 212 MET cc_start: 0.8071 (mmm) cc_final: 0.7444 (mmm) REVERT: A 17 ILE cc_start: 0.8850 (tp) cc_final: 0.8593 (mp) REVERT: E 47 ILE cc_start: 0.9081 (mm) cc_final: 0.8721 (mm) REVERT: E 103 LYS cc_start: 0.8403 (mtmm) cc_final: 0.8194 (mtmm) REVERT: E 143 TYR cc_start: 0.7662 (t80) cc_final: 0.6935 (m-80) REVERT: B 142 ARG cc_start: 0.7592 (pmm-80) cc_final: 0.6976 (ptm160) outliers start: 35 outliers final: 30 residues processed: 185 average time/residue: 0.2029 time to fit residues: 51.9624 Evaluate side-chains 186 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 199 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN A 27 ASN ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8783 Z= 0.342 Angle : 0.662 11.033 11922 Z= 0.327 Chirality : 0.046 0.260 1403 Planarity : 0.004 0.059 1483 Dihedral : 7.714 53.333 1595 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.80 % Allowed : 14.08 % Favored : 81.12 % 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: -1.97 (0.25), residues: 1036 helix: -1.55 (0.67), residues: 64 sheet: -1.07 (0.24), residues: 408 loop : -1.42 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 94 HIS 0.005 0.001 HIS D 122 PHE 0.022 0.002 PHE D 113 TYR 0.017 0.002 TYR E 126 ARG 0.003 0.000 ARG D 176 *********************** 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 195 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 152 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: D 197 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5849 (ptt180) REVERT: D 214 LYS cc_start: 0.8530 (mttt) cc_final: 0.8154 (tmtt) REVERT: C 212 MET cc_start: 0.8161 (mmm) cc_final: 0.7495 (mmm) REVERT: A 17 ILE cc_start: 0.8892 (tp) cc_final: 0.8635 (mp) REVERT: A 27 ASN cc_start: 0.8314 (t0) cc_final: 0.7843 (t0) REVERT: A 89 MET cc_start: 0.8315 (tpt) cc_final: 0.8072 (tpp) REVERT: A 140 MET cc_start: 0.8050 (mtp) cc_final: 0.7785 (mtt) REVERT: E 47 ILE cc_start: 0.9069 (mm) cc_final: 0.8737 (mm) REVERT: E 103 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8180 (mtmm) REVERT: E 143 TYR cc_start: 0.7698 (t80) cc_final: 0.6932 (m-80) REVERT: B 142 ARG cc_start: 0.7928 (pmm-80) cc_final: 0.7149 (ptm160) REVERT: B 212 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7246 (p90) outliers start: 43 outliers final: 36 residues processed: 180 average time/residue: 0.2066 time to fit residues: 51.3003 Evaluate side-chains 184 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 188 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 212 PHE 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: 3.9990 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 78 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN D 80 GLN A 195 GLN E 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 0.027 8783 Z= 0.193 Angle : 0.620 10.343 11922 Z= 0.303 Chirality : 0.044 0.243 1403 Planarity : 0.004 0.055 1483 Dihedral : 7.177 49.676 1595 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.25 % Allowed : 15.20 % Favored : 80.56 % 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: -1.83 (0.25), residues: 1036 helix: -1.44 (0.68), residues: 64 sheet: -1.06 (0.24), residues: 416 loop : -1.25 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 123 HIS 0.003 0.001 HIS D 122 PHE 0.009 0.001 PHE C 64 TYR 0.015 0.001 TYR A 59 ARG 0.001 0.000 ARG B 117 *********************** 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 191 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 153 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 60 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7332 (t0) REVERT: D 80 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8861 (mt0) REVERT: D 214 LYS cc_start: 0.8462 (mttt) cc_final: 0.8082 (tmtt) REVERT: C 212 MET cc_start: 0.8096 (mmm) cc_final: 0.7457 (mmm) REVERT: A 17 ILE cc_start: 0.8889 (tp) cc_final: 0.8634 (mp) REVERT: A 140 MET cc_start: 0.8031 (mtp) cc_final: 0.7788 (mtt) REVERT: E 47 ILE cc_start: 0.9032 (mm) cc_final: 0.8631 (mm) REVERT: E 103 LYS cc_start: 0.8441 (mtmm) cc_final: 0.8201 (mtmm) REVERT: E 143 TYR cc_start: 0.7639 (t80) cc_final: 0.6918 (m-80) REVERT: B 142 ARG cc_start: 0.7908 (pmm-80) cc_final: 0.7146 (ptm160) outliers start: 38 outliers final: 32 residues processed: 178 average time/residue: 0.2124 time to fit residues: 52.0439 Evaluate side-chains 183 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 80 GLN Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 199 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 95 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN A 27 ASN ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8783 Z= 0.244 Angle : 0.620 9.800 11922 Z= 0.306 Chirality : 0.044 0.235 1403 Planarity : 0.004 0.057 1483 Dihedral : 6.914 46.129 1595 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.47 % Allowed : 15.08 % Favored : 80.45 % 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: -1.82 (0.25), residues: 1036 helix: -1.36 (0.69), residues: 64 sheet: -1.03 (0.24), residues: 418 loop : -1.26 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 123 HIS 0.004 0.001 HIS D 122 PHE 0.010 0.001 PHE A 64 TYR 0.016 0.001 TYR A 59 ARG 0.002 0.000 ARG A 73 *********************** 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 189 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 60 ASN cc_start: 0.7688 (OUTLIER) cc_final: 0.7308 (t0) REVERT: D 214 LYS cc_start: 0.8477 (mttt) cc_final: 0.8100 (tmtt) REVERT: C 212 MET cc_start: 0.8125 (mmm) cc_final: 0.7472 (mmm) REVERT: A 17 ILE cc_start: 0.8891 (tp) cc_final: 0.8641 (mp) REVERT: E 47 ILE cc_start: 0.9033 (mm) cc_final: 0.8646 (mm) REVERT: E 103 LYS cc_start: 0.8444 (mtmm) cc_final: 0.8203 (mtmm) REVERT: E 143 TYR cc_start: 0.7647 (t80) cc_final: 0.6925 (m-80) REVERT: B 142 ARG cc_start: 0.7935 (pmm-80) cc_final: 0.7141 (ptm160) REVERT: B 212 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7167 (p90) outliers start: 40 outliers final: 36 residues processed: 175 average time/residue: 0.2057 time to fit residues: 49.7126 Evaluate side-chains 186 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 148 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 212 PHE 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: 0.7980 chunk 68 optimal weight: 0.0030 chunk 102 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN ** A 102 ASN ** 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: 0.8160 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8783 Z= 0.169 Angle : 0.611 11.639 11922 Z= 0.299 Chirality : 0.044 0.214 1403 Planarity : 0.004 0.054 1483 Dihedral : 6.472 42.064 1595 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.91 % Allowed : 15.75 % Favored : 80.34 % 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: -1.70 (0.26), residues: 1036 helix: -1.33 (0.69), residues: 64 sheet: -0.94 (0.24), residues: 416 loop : -1.18 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 123 HIS 0.003 0.001 HIS D 122 PHE 0.009 0.001 PHE C 64 TYR 0.016 0.001 TYR A 59 ARG 0.002 0.000 ARG B 117 ********************** 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 189 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 154 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: D 60 ASN cc_start: 0.7470 (OUTLIER) cc_final: 0.7230 (t0) REVERT: D 214 LYS cc_start: 0.8446 (mttt) cc_final: 0.8073 (tmtt) REVERT: C 212 MET cc_start: 0.8069 (mmm) cc_final: 0.7436 (mmm) REVERT: A 17 ILE cc_start: 0.8886 (tp) cc_final: 0.8635 (mp) REVERT: A 27 ASN cc_start: 0.8027 (t0) cc_final: 0.7707 (t0) REVERT: E 47 ILE cc_start: 0.9015 (mm) cc_final: 0.8617 (mm) REVERT: E 103 LYS cc_start: 0.8432 (mtmm) cc_final: 0.8229 (mtmm) REVERT: E 143 TYR cc_start: 0.7633 (t80) cc_final: 0.6917 (m-80) REVERT: B 142 ARG cc_start: 0.7908 (pmm-80) cc_final: 0.7125 (ptm160) REVERT: B 212 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7172 (p90) outliers start: 35 outliers final: 33 residues processed: 176 average time/residue: 0.2025 time to fit residues: 49.2849 Evaluate side-chains 186 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 189 GLN Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN D 80 GLN E 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.108778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.093997 restraints weight = 16777.889| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.48 r_work: 0.3271 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8783 Z= 0.170 Angle : 0.602 11.404 11922 Z= 0.295 Chirality : 0.043 0.196 1403 Planarity : 0.004 0.054 1483 Dihedral : 6.125 37.921 1595 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 4.13 % Allowed : 16.20 % Favored : 79.66 % 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: -1.62 (0.26), residues: 1036 helix: -1.29 (0.70), residues: 64 sheet: -0.87 (0.24), residues: 416 loop : -1.14 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 123 HIS 0.004 0.001 HIS A 150 PHE 0.009 0.001 PHE A 64 TYR 0.023 0.001 TYR A 59 ARG 0.001 0.000 ARG B 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2442.98 seconds wall clock time: 45 minutes 11.42 seconds (2711.42 seconds total)