Starting phenix.real_space_refine on Sat Feb 17 01:32:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sms_25207/02_2024/7sms_25207_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sms_25207/02_2024/7sms_25207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sms_25207/02_2024/7sms_25207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sms_25207/02_2024/7sms_25207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sms_25207/02_2024/7sms_25207_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sms_25207/02_2024/7sms_25207_updated.pdb" } resolution = 3.18 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= 0.003 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: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 85 5.16 5 C 11202 2.51 5 N 2640 2.21 5 O 3119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17051 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3140 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3456 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 397} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3294 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "D" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3151 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 367} Chain breaks: 1 Chain: "E" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3317 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 386} Chain breaks: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 127 Unusual residues: {'POV': 1, 'TC9': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'CLR': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'CLR': 1, 'POV': 1, 'TC9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'POV': 1, 'TC9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" C1 CLR A 501 " occ=0.80 ... (26 atoms not shown) pdb=" O1 CLR A 501 " occ=0.80 residue: pdb=" N POV B 603 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV B 603 " occ=0.75 residue: pdb=" N POV C 501 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV C 501 " occ=0.75 residue: pdb=" N POV C 502 " occ=0.75 ... (30 atoms not shown) pdb=" P POV C 502 " occ=0.75 residue: pdb=" C1 CLR C 503 " occ=0.89 ... (26 atoms not shown) pdb=" O1 CLR C 503 " occ=0.89 residue: pdb=" C1 CLR D 502 " occ=0.75 ... (26 atoms not shown) pdb=" O1 CLR D 502 " occ=0.75 residue: pdb=" N POV D 503 " occ=0.75 ... (33 atoms not shown) pdb="C311 POV D 503 " occ=0.75 residue: pdb=" N POV E 602 " occ=0.75 ... (38 atoms not shown) pdb="C215 POV E 602 " occ=0.75 Time building chain proxies: 9.79, per 1000 atoms: 0.57 Number of scatterers: 17051 At special positions: 0 Unit cell: (162.549, 125.12, 100.524, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 5 15.00 O 3119 8.00 N 2640 7.00 C 11202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.04 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.07 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 ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 143 " " NAG H 1 " - " ASN C 141 " " NAG I 1 " - " ASN D 141 " " NAG J 1 " - " ASN E 141 " Time building additional restraints: 7.34 Conformation dependent library (CDL) restraints added in 3.2 seconds 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 23 sheets defined 39.4% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 219 through 234 removed outlier: 3.586A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR A 229 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 242 through 262 Processing helix chain 'A' and resid 273 through 299 Processing helix chain 'A' and resid 310 through 316 removed outlier: 3.739A pdb=" N ILE A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 425 Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 233 through 248 removed outlier: 3.563A pdb=" N ALA B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N TYR B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 256 through 277 Processing helix chain 'B' and resid 287 through 313 Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 334 through 337 No H-bonds generated for 'chain 'B' and resid 334 through 337' Processing helix chain 'B' and resid 417 through 475 Proline residue: B 463 - end of helix Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 69 through 72 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 218 through 239 removed outlier: 4.679A pdb=" N ILE C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix removed outlier: 4.674A pdb=" N PHE C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 245 No H-bonds generated for 'chain 'C' and resid 243 through 245' Processing helix chain 'C' and resid 248 through 268 removed outlier: 4.000A pdb=" N ASP C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 305 Processing helix chain 'C' and resid 316 through 322 Processing helix chain 'C' and resid 326 through 330 Processing helix chain 'C' and resid 399 through 459 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 69 through 72 Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 212 through 234 removed outlier: 4.687A pdb=" N ILE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 4.136A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N PHE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TYR D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 242 through 261 Processing helix chain 'D' and resid 273 through 299 Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 320 through 323 No H-bonds generated for 'chain 'D' and resid 320 through 323' Processing helix chain 'D' and resid 371 through 425 Processing helix chain 'E' and resid 4 through 12 Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 220 through 225 Processing helix chain 'E' and resid 227 through 241 removed outlier: 3.773A pdb=" N LEU E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 271 Processing helix chain 'E' and resid 282 through 308 Processing helix chain 'E' and resid 319 through 327 Processing helix chain 'E' and resid 412 through 471 removed outlier: 3.610A pdb=" N LEU E 457 " --> pdb=" O TRP E 453 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 156 through 160 removed outlier: 5.974A pdb=" N VAL A 29 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N SER A 159 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 31 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP A 30 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE A 61 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN A 53 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU A 40 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLU A 51 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= C, first strand: chain 'A' and resid 77 through 80 Processing sheet with id= D, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.557A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 31 through 33 Processing sheet with id= F, first strand: chain 'B' and resid 44 through 46 Processing sheet with id= G, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.186A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 164 through 166 Processing sheet with id= I, first strand: chain 'B' and resid 34 through 42 removed outlier: 3.546A pdb=" N SER B 36 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 190 through 194 removed outlier: 6.921A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 156 through 160 removed outlier: 6.252A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N THR C 30 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR C 61 " --> pdb=" O THR C 30 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C 53 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 42 through 44 Processing sheet with id= M, first strand: chain 'C' and resid 77 through 80 Processing sheet with id= N, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.400A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 186 through 190 removed outlier: 6.825A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 156 through 160 removed outlier: 5.991A pdb=" N VAL D 29 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N SER D 159 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE D 31 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP D 30 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE D 61 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN D 53 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU D 40 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU D 51 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 42 through 44 Processing sheet with id= R, first strand: chain 'D' and resid 77 through 81 Processing sheet with id= S, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.614A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE D 205 " --> pdb=" O CYS D 142 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP D 180 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN D 208 " --> pdb=" O MET D 178 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N MET D 178 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 42 through 44 removed outlier: 3.825A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU E 119 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN E 107 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.204A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 32 through 40 removed outlier: 6.834A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 184 through 188 removed outlier: 6.844A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) 785 hydrogen bonds defined for protein. 2292 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: 4.78 Time building geometry restraints manager: 7.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2633 1.31 - 1.45: 4895 1.45 - 1.58: 9844 1.58 - 1.71: 10 1.71 - 1.84: 139 Bond restraints: 17521 Sorted by residual: bond pdb=" C19 TC9 B 602 " pdb=" C24 TC9 B 602 " ideal model delta sigma weight residual 1.519 1.393 0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C19 TC9 E 601 " pdb=" C24 TC9 E 601 " ideal model delta sigma weight residual 1.519 1.393 0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" C19 TC9 B 601 " pdb=" C24 TC9 B 601 " ideal model delta sigma weight residual 1.519 1.394 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C19 TC9 D 501 " pdb=" C24 TC9 D 501 " ideal model delta sigma weight residual 1.519 1.395 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" C19 TC9 E 601 " pdb=" N20 TC9 E 601 " ideal model delta sigma weight residual 1.540 1.482 0.058 2.00e-02 2.50e+03 8.35e+00 ... (remaining 17516 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.27: 395 105.27 - 112.46: 9513 112.46 - 119.66: 5688 119.66 - 126.85: 8027 126.85 - 134.05: 307 Bond angle restraints: 23930 Sorted by residual: angle pdb=" O11 POV C 502 " pdb=" P POV C 502 " pdb=" O12 POV C 502 " ideal model delta sigma weight residual 97.67 110.10 -12.43 3.00e+00 1.11e-01 1.72e+01 angle pdb=" O11 POV B 603 " pdb=" P POV B 603 " pdb=" O12 POV B 603 " ideal model delta sigma weight residual 97.67 109.37 -11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O13 POV B 603 " pdb=" P POV B 603 " pdb=" O14 POV B 603 " ideal model delta sigma weight residual 121.11 109.47 11.64 3.00e+00 1.11e-01 1.51e+01 angle pdb=" O13 POV E 602 " pdb=" P POV E 602 " pdb=" O14 POV E 602 " ideal model delta sigma weight residual 121.11 109.51 11.60 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O13 POV D 503 " pdb=" P POV D 503 " pdb=" O14 POV D 503 " ideal model delta sigma weight residual 121.11 109.52 11.59 3.00e+00 1.11e-01 1.49e+01 ... (remaining 23925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.02: 10468 31.02 - 62.05: 281 62.05 - 93.07: 88 93.07 - 124.10: 29 124.10 - 155.12: 6 Dihedral angle restraints: 10872 sinusoidal: 4892 harmonic: 5980 Sorted by residual: dihedral pdb=" CA CYS D 142 " pdb=" C CYS D 142 " pdb=" N THR D 143 " pdb=" CA THR D 143 " ideal model delta harmonic sigma weight residual 180.00 -151.41 -28.59 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N CYS A 193 " pdb=" CA CYS A 193 " ideal model delta harmonic sigma weight residual -180.00 -151.79 -28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA CYS A 142 " pdb=" C CYS A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 10869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2324 0.060 - 0.119: 406 0.119 - 0.179: 53 0.179 - 0.238: 7 0.238 - 0.298: 7 Chirality restraints: 2797 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 141 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2794 not shown) Planarity restraints: 2887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 TC9 E 601 " -0.014 2.00e-02 2.50e+03 1.05e-02 3.04e+00 pdb=" C22 TC9 E 601 " 0.009 2.00e-02 2.50e+03 pdb=" C23 TC9 E 601 " -0.012 2.00e-02 2.50e+03 pdb=" C24 TC9 E 601 " 0.019 2.00e-02 2.50e+03 pdb=" C25 TC9 E 601 " 0.001 2.00e-02 2.50e+03 pdb=" C26 TC9 E 601 " 0.000 2.00e-02 2.50e+03 pdb=" C27 TC9 E 601 " -0.002 2.00e-02 2.50e+03 pdb=" C28 TC9 E 601 " -0.016 2.00e-02 2.50e+03 pdb=" O29 TC9 E 601 " 0.014 2.00e-02 2.50e+03 pdb=" O40 TC9 E 601 " 0.001 2.00e-02 2.50e+03 pdb=" O42 TC9 E 601 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C19 TC9 B 601 " -0.015 2.00e-02 2.50e+03 9.83e-03 2.66e+00 pdb=" C22 TC9 B 601 " 0.009 2.00e-02 2.50e+03 pdb=" C23 TC9 B 601 " -0.011 2.00e-02 2.50e+03 pdb=" C24 TC9 B 601 " 0.019 2.00e-02 2.50e+03 pdb=" C25 TC9 B 601 " 0.001 2.00e-02 2.50e+03 pdb=" C26 TC9 B 601 " 0.001 2.00e-02 2.50e+03 pdb=" C27 TC9 B 601 " -0.001 2.00e-02 2.50e+03 pdb=" C28 TC9 B 601 " -0.013 2.00e-02 2.50e+03 pdb=" O29 TC9 B 601 " 0.010 2.00e-02 2.50e+03 pdb=" O40 TC9 B 601 " -0.003 2.00e-02 2.50e+03 pdb=" O42 TC9 B 601 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 221 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C ILE C 221 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE C 221 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL C 222 " 0.009 2.00e-02 2.50e+03 ... (remaining 2884 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 958 2.73 - 3.27: 16958 3.27 - 3.81: 28314 3.81 - 4.36: 34631 4.36 - 4.90: 59841 Nonbonded interactions: 140702 Sorted by model distance: nonbonded pdb=" OE2 GLU D 45 " pdb=" NH2 ARG D 209 " model vdw 2.187 2.520 nonbonded pdb=" OG SER B 494 " pdb=" OD1 ASP B 496 " model vdw 2.202 2.440 nonbonded pdb=" OD2 ASP B 140 " pdb=" NE2 GLN B 142 " model vdw 2.211 2.520 nonbonded pdb=" OE2 GLU B 191 " pdb=" NH2 ARG B 222 " model vdw 2.235 2.520 nonbonded pdb=" OD2 ASP C 138 " pdb=" NE2 GLN C 140 " model vdw 2.239 2.520 ... (remaining 140697 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 1 through 426) selection = (chain 'D' and (resid 1 through 330 or resid 370 through 426)) } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'J' } 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=0.75 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: 1.010 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: 0.020 Extract box with map and model: 4.440 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 48.240 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 0.126 17521 Z= 0.406 Angle : 0.779 12.431 23930 Z= 0.342 Chirality : 0.049 0.298 2797 Planarity : 0.004 0.034 2882 Dihedral : 17.585 155.120 6957 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.21 (0.19), residues: 1995 helix: 2.85 (0.18), residues: 756 sheet: -0.69 (0.24), residues: 422 loop : -0.28 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 60 HIS 0.005 0.001 HIS B 60 PHE 0.014 0.001 PHE D 256 TYR 0.011 0.001 TYR B 439 ARG 0.005 0.001 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 293 PHE cc_start: 0.8312 (m-80) cc_final: 0.7897 (m-10) REVERT: D 226 SER cc_start: 0.8905 (m) cc_final: 0.8510 (p) REVERT: D 227 PHE cc_start: 0.7950 (t80) cc_final: 0.7200 (m-80) REVERT: D 325 PHE cc_start: 0.6617 (m-80) cc_final: 0.6397 (m-80) REVERT: E 317 LEU cc_start: 0.8513 (tp) cc_final: 0.8310 (tp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2812 time to fit residues: 65.0049 Evaluate side-chains 105 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 4.9990 chunk 150 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN D 408 HIS E 95 ASN E 271 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17521 Z= 0.175 Angle : 0.532 8.150 23930 Z= 0.253 Chirality : 0.042 0.194 2797 Planarity : 0.003 0.034 2882 Dihedral : 14.569 130.598 3048 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.43 % Allowed : 3.65 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.43 (0.20), residues: 1995 helix: 3.02 (0.18), residues: 758 sheet: -0.47 (0.25), residues: 417 loop : -0.23 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 60 HIS 0.003 0.000 HIS A 204 PHE 0.012 0.001 PHE D 256 TYR 0.010 0.001 TYR B 439 ARG 0.004 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 293 PHE cc_start: 0.8287 (m-80) cc_final: 0.7887 (m-10) REVERT: D 227 PHE cc_start: 0.7938 (t80) cc_final: 0.7087 (m-80) REVERT: E 116 MET cc_start: 0.7776 (mmt) cc_final: 0.7553 (mmt) REVERT: E 299 MET cc_start: 0.7183 (ttt) cc_final: 0.6785 (ttp) REVERT: E 317 LEU cc_start: 0.8574 (tp) cc_final: 0.8343 (tp) REVERT: E 448 ASP cc_start: 0.8233 (t0) cc_final: 0.7934 (m-30) outliers start: 8 outliers final: 4 residues processed: 117 average time/residue: 0.2739 time to fit residues: 52.6682 Evaluate side-chains 103 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 132 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN E 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17521 Z= 0.276 Angle : 0.540 7.120 23930 Z= 0.259 Chirality : 0.044 0.191 2797 Planarity : 0.003 0.035 2882 Dihedral : 12.761 126.068 3048 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.70 % Allowed : 6.28 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.43 (0.19), residues: 1995 helix: 2.99 (0.18), residues: 755 sheet: -0.41 (0.25), residues: 406 loop : -0.24 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 60 HIS 0.004 0.001 HIS B 60 PHE 0.016 0.001 PHE D 325 TYR 0.011 0.001 TYR B 439 ARG 0.003 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 293 PHE cc_start: 0.8301 (m-80) cc_final: 0.7892 (m-10) REVERT: C 436 ASP cc_start: 0.8072 (t0) cc_final: 0.7829 (t0) REVERT: D 227 PHE cc_start: 0.7975 (t80) cc_final: 0.7029 (m-80) REVERT: E 299 MET cc_start: 0.7261 (ttt) cc_final: 0.6827 (ttp) REVERT: E 317 LEU cc_start: 0.8458 (tp) cc_final: 0.8210 (tp) REVERT: E 448 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7949 (m-30) outliers start: 13 outliers final: 5 residues processed: 114 average time/residue: 0.2580 time to fit residues: 48.6481 Evaluate side-chains 105 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17521 Z= 0.253 Angle : 0.516 7.173 23930 Z= 0.249 Chirality : 0.043 0.208 2797 Planarity : 0.003 0.036 2882 Dihedral : 11.794 129.319 3048 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.81 % Allowed : 7.35 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.46 (0.19), residues: 1995 helix: 3.04 (0.18), residues: 757 sheet: -0.38 (0.25), residues: 393 loop : -0.26 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 60 HIS 0.003 0.001 HIS B 60 PHE 0.013 0.001 PHE D 256 TYR 0.011 0.001 TYR E 117 ARG 0.002 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 2.222 Fit side-chains revert: symmetry clash REVERT: C 293 PHE cc_start: 0.8306 (m-80) cc_final: 0.7894 (m-10) REVERT: C 436 ASP cc_start: 0.8038 (t0) cc_final: 0.7772 (t0) REVERT: E 299 MET cc_start: 0.7275 (ttt) cc_final: 0.6850 (ttp) REVERT: E 317 LEU cc_start: 0.8483 (tp) cc_final: 0.8228 (tp) REVERT: E 448 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7986 (m-30) outliers start: 15 outliers final: 6 residues processed: 117 average time/residue: 0.2587 time to fit residues: 50.1832 Evaluate side-chains 107 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 142 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 171 optimal weight: 0.2980 chunk 48 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN E 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17521 Z= 0.147 Angle : 0.475 7.012 23930 Z= 0.231 Chirality : 0.042 0.194 2797 Planarity : 0.003 0.037 2882 Dihedral : 11.207 131.219 3048 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.48 % Allowed : 8.59 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.66 (0.19), residues: 1995 helix: 3.19 (0.18), residues: 762 sheet: -0.23 (0.26), residues: 389 loop : -0.18 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 60 HIS 0.003 0.000 HIS D 134 PHE 0.022 0.001 PHE D 227 TYR 0.010 0.001 TYR E 117 ARG 0.002 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 110 time to evaluate : 1.957 Fit side-chains REVERT: C 133 MET cc_start: 0.7975 (ttm) cc_final: 0.7751 (ttm) REVERT: C 293 PHE cc_start: 0.8260 (m-80) cc_final: 0.7888 (m-10) REVERT: C 436 ASP cc_start: 0.8115 (t0) cc_final: 0.7822 (t0) REVERT: C 468 PHE cc_start: 0.7860 (m-80) cc_final: 0.7645 (m-80) REVERT: D 227 PHE cc_start: 0.7884 (t80) cc_final: 0.7028 (m-80) REVERT: E 299 MET cc_start: 0.7265 (ttt) cc_final: 0.6714 (ttp) REVERT: E 317 LEU cc_start: 0.8450 (tp) cc_final: 0.8198 (tp) REVERT: E 448 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.8013 (m-30) outliers start: 9 outliers final: 5 residues processed: 116 average time/residue: 0.2638 time to fit residues: 49.6378 Evaluate side-chains 108 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS E 95 ASN E 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17521 Z= 0.399 Angle : 0.562 7.284 23930 Z= 0.272 Chirality : 0.044 0.205 2797 Planarity : 0.003 0.037 2882 Dihedral : 11.226 129.599 3048 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.81 % Allowed : 9.18 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.45 (0.19), residues: 1995 helix: 2.98 (0.18), residues: 763 sheet: -0.35 (0.25), residues: 398 loop : -0.26 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.006 0.001 HIS B 60 PHE 0.016 0.001 PHE D 227 TYR 0.013 0.001 TYR B 439 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 2.292 Fit side-chains REVERT: C 293 PHE cc_start: 0.8330 (m-80) cc_final: 0.7925 (m-10) REVERT: C 436 ASP cc_start: 0.8112 (t0) cc_final: 0.7782 (t0) REVERT: C 468 PHE cc_start: 0.7926 (m-80) cc_final: 0.7720 (m-80) REVERT: D 227 PHE cc_start: 0.7943 (t80) cc_final: 0.7103 (m-80) REVERT: E 317 LEU cc_start: 0.8546 (tp) cc_final: 0.8291 (tp) REVERT: E 448 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.8001 (m-30) outliers start: 15 outliers final: 8 residues processed: 121 average time/residue: 0.2622 time to fit residues: 52.2646 Evaluate side-chains 108 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 190 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17521 Z= 0.215 Angle : 0.497 7.082 23930 Z= 0.241 Chirality : 0.042 0.185 2797 Planarity : 0.003 0.037 2882 Dihedral : 11.036 130.196 3048 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.59 % Allowed : 10.04 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.58 (0.19), residues: 1995 helix: 3.13 (0.18), residues: 762 sheet: -0.29 (0.25), residues: 395 loop : -0.23 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.004 0.001 HIS B 60 PHE 0.016 0.001 PHE D 227 TYR 0.010 0.001 TYR B 439 ARG 0.001 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 2.236 Fit side-chains REVERT: A 208 GLN cc_start: 0.8116 (tp40) cc_final: 0.7588 (tp40) REVERT: C 293 PHE cc_start: 0.8298 (m-80) cc_final: 0.7908 (m-10) REVERT: C 436 ASP cc_start: 0.8177 (t0) cc_final: 0.7844 (t0) REVERT: C 468 PHE cc_start: 0.7872 (m-80) cc_final: 0.7670 (m-80) REVERT: D 227 PHE cc_start: 0.7899 (t80) cc_final: 0.7059 (m-80) REVERT: E 299 MET cc_start: 0.7310 (ttt) cc_final: 0.6771 (ttp) REVERT: E 317 LEU cc_start: 0.8538 (tp) cc_final: 0.8287 (tp) REVERT: E 448 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.8008 (m-30) outliers start: 11 outliers final: 7 residues processed: 110 average time/residue: 0.2627 time to fit residues: 47.5997 Evaluate side-chains 108 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 chunk 150 optimal weight: 0.0670 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 HIS E 95 ASN E 431 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17521 Z= 0.137 Angle : 0.463 6.925 23930 Z= 0.225 Chirality : 0.041 0.183 2797 Planarity : 0.003 0.037 2882 Dihedral : 10.711 130.946 3048 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.64 % Allowed : 9.98 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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 (0.19), residues: 1995 helix: 3.31 (0.18), residues: 757 sheet: -0.17 (0.26), residues: 389 loop : -0.19 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 60 HIS 0.003 0.000 HIS D 385 PHE 0.017 0.001 PHE D 227 TYR 0.009 0.001 TYR B 439 ARG 0.002 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 2.172 Fit side-chains REVERT: A 178 MET cc_start: 0.8987 (mmp) cc_final: 0.8657 (tpp) REVERT: C 133 MET cc_start: 0.7955 (ttm) cc_final: 0.7736 (ttm) REVERT: C 293 PHE cc_start: 0.8256 (m-80) cc_final: 0.7891 (m-10) REVERT: C 436 ASP cc_start: 0.8102 (t0) cc_final: 0.7773 (t0) REVERT: D 227 PHE cc_start: 0.7848 (t80) cc_final: 0.6970 (m-80) REVERT: D 324 MET cc_start: 0.6436 (mmm) cc_final: 0.6145 (mmt) REVERT: D 408 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.6774 (t70) REVERT: E 299 MET cc_start: 0.7263 (ttt) cc_final: 0.6732 (ttp) REVERT: E 317 LEU cc_start: 0.8534 (tp) cc_final: 0.8231 (tp) REVERT: E 448 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.8025 (m-30) outliers start: 12 outliers final: 6 residues processed: 116 average time/residue: 0.2458 time to fit residues: 47.2688 Evaluate side-chains 112 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.0870 chunk 182 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 139 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 ASN E 431 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17521 Z= 0.146 Angle : 0.465 6.930 23930 Z= 0.225 Chirality : 0.041 0.184 2797 Planarity : 0.003 0.037 2882 Dihedral : 10.642 131.008 3048 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.54 % Allowed : 10.68 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.77 (0.19), residues: 1995 helix: 3.30 (0.18), residues: 762 sheet: -0.16 (0.25), residues: 396 loop : -0.14 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 60 HIS 0.003 0.000 HIS D 408 PHE 0.016 0.001 PHE D 227 TYR 0.009 0.001 TYR B 439 ARG 0.002 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 2.017 Fit side-chains REVERT: A 178 MET cc_start: 0.8988 (mmp) cc_final: 0.8664 (tpp) REVERT: C 133 MET cc_start: 0.7952 (ttm) cc_final: 0.7726 (ttm) REVERT: C 293 PHE cc_start: 0.8247 (m-80) cc_final: 0.7869 (m-10) REVERT: C 436 ASP cc_start: 0.8132 (t0) cc_final: 0.7774 (t0) REVERT: E 299 MET cc_start: 0.7272 (ttt) cc_final: 0.6741 (ttp) REVERT: E 317 LEU cc_start: 0.8542 (tp) cc_final: 0.8237 (tp) REVERT: E 448 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.8012 (m-30) outliers start: 10 outliers final: 6 residues processed: 111 average time/residue: 0.2479 time to fit residues: 45.8736 Evaluate side-chains 111 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 89 optimal weight: 0.4980 chunk 130 optimal weight: 4.9990 chunk 197 optimal weight: 0.6980 chunk 181 optimal weight: 0.0870 chunk 157 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 ASN E 431 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17521 Z= 0.136 Angle : 0.460 6.907 23930 Z= 0.223 Chirality : 0.041 0.184 2797 Planarity : 0.003 0.037 2882 Dihedral : 10.466 130.747 3048 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.64 % Allowed : 10.57 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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: 1.85 (0.19), residues: 1995 helix: 3.37 (0.18), residues: 762 sheet: -0.17 (0.25), residues: 406 loop : -0.07 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 60 HIS 0.004 0.000 HIS D 385 PHE 0.023 0.001 PHE D 227 TYR 0.009 0.001 TYR B 439 ARG 0.002 0.000 ARG C 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 2.058 Fit side-chains REVERT: A 178 MET cc_start: 0.8979 (mmp) cc_final: 0.8685 (tpp) REVERT: C 133 MET cc_start: 0.7933 (ttm) cc_final: 0.7705 (ttm) REVERT: C 293 PHE cc_start: 0.8229 (m-80) cc_final: 0.7849 (m-10) REVERT: C 436 ASP cc_start: 0.8125 (t0) cc_final: 0.7747 (t0) REVERT: D 408 HIS cc_start: 0.7385 (OUTLIER) cc_final: 0.6380 (t-90) REVERT: E 299 MET cc_start: 0.7272 (ttt) cc_final: 0.6745 (ttp) REVERT: E 317 LEU cc_start: 0.8549 (tp) cc_final: 0.8241 (tp) REVERT: E 448 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.8021 (m-30) REVERT: E 467 PHE cc_start: 0.6899 (m-10) cc_final: 0.6522 (t80) outliers start: 12 outliers final: 8 residues processed: 121 average time/residue: 0.2484 time to fit residues: 49.9449 Evaluate side-chains 111 residues out of total 1863 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 408 HIS Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.0870 chunk 48 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 157 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 0.0060 chunk 138 optimal weight: 6.9990 overall best weight: 0.6976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 ASN ** E 431 ASN ** 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 = 0.3295 r_free = 0.3295 target = 0.096152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.074603 restraints weight = 29896.778| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.53 r_work: 0.2804 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17521 Z= 0.150 Angle : 0.465 7.792 23930 Z= 0.226 Chirality : 0.041 0.184 2797 Planarity : 0.003 0.037 2882 Dihedral : 10.379 130.321 3048 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.54 % Allowed : 10.79 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.19), residues: 1995 helix: 3.37 (0.18), residues: 762 sheet: -0.16 (0.25), residues: 406 loop : -0.05 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 60 HIS 0.003 0.000 HIS D 204 PHE 0.023 0.001 PHE D 227 TYR 0.009 0.001 TYR B 439 ARG 0.002 0.000 ARG A 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3114.65 seconds wall clock time: 58 minutes 4.03 seconds (3484.03 seconds total)