Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 14:51:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huk_0280/04_2023/6huk_0280_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huk_0280/04_2023/6huk_0280.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huk_0280/04_2023/6huk_0280_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huk_0280/04_2023/6huk_0280_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huk_0280/04_2023/6huk_0280_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huk_0280/04_2023/6huk_0280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huk_0280/04_2023/6huk_0280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huk_0280/04_2023/6huk_0280_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6huk_0280/04_2023/6huk_0280_updated.pdb" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 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 6 5.49 5 S 83 5.16 5 C 9892 2.51 5 N 2481 2.21 5 O 2838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "C ARG 324": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 180": "NH1" <-> "NH2" Residue "E ARG 269": "NH1" <-> "NH2" Residue "E TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 15300 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2809 Classifications: {'peptide': 347} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 332} Chain breaks: 1 Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2758 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2720 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2812 Classifications: {'peptide': 347} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 332} Chain breaks: 1 Chain: "E" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2740 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 Chain: "G" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "F" 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 chiralities: 7 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" 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 chiralities: 5 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'H0Z': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'H0Z': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.23, per 1000 atoms: 0.54 Number of scatterers: 15300 At special positions: 0 Unit cell: (100.58, 124.12, 138.03, 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 83 16.00 P 6 15.00 O 2838 8.00 N 2481 7.00 C 9892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.02 Simple disulfide: pdb=" SG CYS G 428 " - pdb=" SG CYS G 501 " 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=1, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 5 " " BMA M 3 " - " MAN M 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG F 1 " - " ASN A 111 " " NAG H 1 " - " ASN B 80 " " NAG I 1 " - " ASN B 149 " " NAG J 1 " - " ASN C 208 " " NAG K 1 " - " ASN D 111 " " NAG L 1 " - " ASN E 80 " " NAG M 1 " - " ASN E 149 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.67 Conformation dependent library (CDL) restraints added in 2.2 seconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3436 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 25 sheets defined 31.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 88 through 91 No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 175 through 178 No H-bonds generated for 'chain 'A' and resid 175 through 178' Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 231 through 246 removed outlier: 5.058A pdb=" N PHE A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TRP A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 275 Processing helix chain 'A' and resid 285 through 310 removed outlier: 3.608A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 415 removed outlier: 4.013A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.613A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 241 removed outlier: 3.872A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.939A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 306 removed outlier: 3.542A pdb=" N LEU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 445 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 241 through 256 removed outlier: 4.302A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 280 Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 295 through 319 Processing helix chain 'C' and resid 407 through 434 removed outlier: 5.713A pdb=" N ASP C 411 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG C 415 " --> pdb=" O SER C 412 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N PHE C 418 " --> pdb=" O ARG C 415 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.522A pdb=" N LEU C 424 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 428 " --> pdb=" O PHE C 425 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 429 " --> pdb=" O ASN C 426 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP C 430 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 431 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 433 " --> pdb=" O TRP C 430 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 434 " --> pdb=" O VAL C 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 88 through 93 removed outlier: 4.222A pdb=" N LYS D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 178 No H-bonds generated for 'chain 'D' and resid 175 through 178' Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 231 through 246 removed outlier: 3.948A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 274 removed outlier: 3.875A pdb=" N VAL D 263 " --> pdb=" O GLY D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 308 Processing helix chain 'D' and resid 391 through 414 removed outlier: 3.529A pdb=" N ARG D 397 " --> pdb=" O ASP D 393 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) Proline residue: D 401 - end of helix Processing helix chain 'E' and resid 10 through 19 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 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 226 through 241 removed outlier: 3.784A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 271 Processing helix chain 'E' and resid 280 through 306 removed outlier: 3.586A pdb=" N TYR E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 445 removed outlier: 3.806A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 167 through 169 removed outlier: 5.730A pdb=" N THR A 39 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 64 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP A 70 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 99 through 101 Processing sheet with id= D, first strand: chain 'A' and resid 150 through 155 Processing sheet with id= E, first strand: chain 'A' and resid 196 through 204 removed outlier: 3.558A pdb=" N TYR A 210 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.274A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.619A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 114 through 118 removed outlier: 3.558A pdb=" N GLY B 127 " --> pdb=" O MET B 115 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 186 through 188 Processing sheet with id= J, first strand: chain 'C' and resid 179 through 183 removed outlier: 5.804A pdb=" N THR C 51 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLN C 182 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE C 53 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= L, first strand: chain 'C' and resid 111 through 113 Processing sheet with id= M, first strand: chain 'C' and resid 163 through 165 removed outlier: 3.622A pdb=" N SER C 224 " --> pdb=" O THR C 209 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 116 through 121 removed outlier: 6.696A pdb=" N ASP C 148 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA C 119 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR C 146 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.149A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 83 through 85 Processing sheet with id= Q, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= R, first strand: chain 'D' and resid 150 through 154 Processing sheet with id= S, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.470A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP E 43 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 65 through 68 removed outlier: 3.704A pdb=" N TRP E 67 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 151 through 155 Processing sheet with id= V, first strand: chain 'E' and resid 186 through 188 Processing sheet with id= W, first strand: chain 'G' and resid 3 through 6 Processing sheet with id= X, first strand: chain 'G' and resid 523 through 525 removed outlier: 3.614A pdb=" N MET G 440 " --> pdb=" O MET G 457 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ARG G 444 " --> pdb=" O PHE G 453 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N PHE G 453 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA G 446 " --> pdb=" O ARG G 451 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG G 451 " --> pdb=" O ALA G 446 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 502 through 504 574 hydrogen bonds defined for protein. 1644 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: 4.70 Time building geometry restraints manager: 7.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2440 1.32 - 1.45: 4639 1.45 - 1.57: 8461 1.57 - 1.69: 9 1.69 - 1.81: 143 Bond restraints: 15692 Sorted by residual: bond pdb=" C1B PIO A 502 " pdb=" O3C PIO A 502 " ideal model delta sigma weight residual 1.399 1.333 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C2C PIO D 501 " pdb=" O2C PIO D 501 " ideal model delta sigma weight residual 1.399 1.463 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" O13 PIO A 502 " pdb=" P1 PIO A 502 " ideal model delta sigma weight residual 1.648 1.585 0.063 2.00e-02 2.50e+03 9.87e+00 bond pdb=" C1B PIO D 501 " pdb=" O3C PIO D 501 " ideal model delta sigma weight residual 1.399 1.336 0.063 2.00e-02 2.50e+03 9.80e+00 bond pdb=" C2C PIO A 502 " pdb=" O2C PIO A 502 " ideal model delta sigma weight residual 1.399 1.462 -0.063 2.00e-02 2.50e+03 9.77e+00 ... (remaining 15687 not shown) Histogram of bond angle deviations from ideal: 94.00 - 102.27: 66 102.27 - 110.54: 4557 110.54 - 118.82: 7942 118.82 - 127.09: 8569 127.09 - 135.36: 204 Bond angle restraints: 21338 Sorted by residual: angle pdb=" C VAL D 64 " pdb=" CA VAL D 64 " pdb=" CB VAL D 64 " ideal model delta sigma weight residual 110.62 99.50 11.12 1.49e+00 4.50e-01 5.57e+01 angle pdb=" N ASN D 417 " pdb=" CA ASN D 417 " pdb=" C ASN D 417 " ideal model delta sigma weight residual 113.50 106.13 7.37 1.23e+00 6.61e-01 3.59e+01 angle pdb=" N VAL E 87 " pdb=" CA VAL E 87 " pdb=" C VAL E 87 " ideal model delta sigma weight residual 113.22 106.14 7.08 1.23e+00 6.61e-01 3.31e+01 angle pdb=" N VAL D 64 " pdb=" CA VAL D 64 " pdb=" C VAL D 64 " ideal model delta sigma weight residual 108.48 116.74 -8.26 1.44e+00 4.82e-01 3.29e+01 angle pdb=" N ASN A 275 " pdb=" CA ASN A 275 " pdb=" C ASN A 275 " ideal model delta sigma weight residual 111.28 116.89 -5.61 1.09e+00 8.42e-01 2.65e+01 ... (remaining 21333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.00: 8781 22.00 - 43.99: 141 43.99 - 65.99: 18 65.99 - 87.99: 2 87.99 - 109.98: 4 Dihedral angle restraints: 8946 sinusoidal: 3603 harmonic: 5343 Sorted by residual: 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 93.00 143.27 -50.27 1 1.00e+01 1.00e-02 3.46e+01 dihedral pdb=" CA ARG C 231 " pdb=" C ARG C 231 " pdb=" N ARG C 232 " pdb=" CA ARG C 232 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA VAL A 64 " pdb=" C VAL A 64 " pdb=" N PHE A 65 " pdb=" CA PHE A 65 " ideal model delta harmonic sigma weight residual 180.00 151.05 28.95 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 8943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2341 0.112 - 0.223: 124 0.223 - 0.335: 9 0.335 - 0.447: 3 0.447 - 0.559: 3 Chirality restraints: 2480 Sorted by residual: chirality pdb=" C1 MAN F 4 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 4 " pdb=" O5 MAN F 4 " both_signs ideal model delta sigma weight residual False 2.40 1.98 0.42 2.00e-02 2.50e+03 4.34e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.12e+02 chirality pdb=" C1 MAN F 7 " pdb=" O3 BMA F 3 " pdb=" C2 MAN F 7 " pdb=" O5 MAN F 7 " both_signs ideal model delta sigma weight residual False 2.40 2.05 0.35 2.00e-02 2.50e+03 3.05e+02 ... (remaining 2477 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 H0Z E 501 " 0.098 2.00e-02 2.50e+03 4.91e-02 6.02e+01 pdb=" C06 H0Z E 501 " -0.019 2.00e-02 2.50e+03 pdb=" C07 H0Z E 501 " -0.003 2.00e-02 2.50e+03 pdb=" C08 H0Z E 501 " 0.037 2.00e-02 2.50e+03 pdb=" C09 H0Z E 501 " 0.022 2.00e-02 2.50e+03 pdb=" C13 H0Z E 501 " -0.026 2.00e-02 2.50e+03 pdb=" C14 H0Z E 501 " -0.048 2.00e-02 2.50e+03 pdb=" C15 H0Z E 501 " -0.076 2.00e-02 2.50e+03 pdb=" O10 H0Z E 501 " 0.048 2.00e-02 2.50e+03 pdb=" O12 H0Z E 501 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 H0Z A 501 " -0.047 2.00e-02 2.50e+03 3.13e-02 2.46e+01 pdb=" C06 H0Z A 501 " 0.005 2.00e-02 2.50e+03 pdb=" C07 H0Z A 501 " -0.007 2.00e-02 2.50e+03 pdb=" C08 H0Z A 501 " -0.042 2.00e-02 2.50e+03 pdb=" C09 H0Z A 501 " -0.024 2.00e-02 2.50e+03 pdb=" C13 H0Z A 501 " 0.011 2.00e-02 2.50e+03 pdb=" C14 H0Z A 501 " 0.020 2.00e-02 2.50e+03 pdb=" C15 H0Z A 501 " 0.062 2.00e-02 2.50e+03 pdb=" O10 H0Z A 501 " -0.008 2.00e-02 2.50e+03 pdb=" O12 H0Z A 501 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 H0Z E 501 " -0.063 2.00e-02 2.50e+03 3.00e-02 2.26e+01 pdb=" C18 H0Z E 501 " 0.058 2.00e-02 2.50e+03 pdb=" C20 H0Z E 501 " 0.004 2.00e-02 2.50e+03 pdb=" C21 H0Z E 501 " -0.006 2.00e-02 2.50e+03 pdb=" C25 H0Z E 501 " 0.001 2.00e-02 2.50e+03 pdb=" C26 H0Z E 501 " 0.018 2.00e-02 2.50e+03 pdb=" C27 H0Z E 501 " 0.020 2.00e-02 2.50e+03 pdb=" C28 H0Z E 501 " 0.006 2.00e-02 2.50e+03 pdb=" O22 H0Z E 501 " -0.029 2.00e-02 2.50e+03 pdb=" O24 H0Z E 501 " -0.009 2.00e-02 2.50e+03 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2087 2.76 - 3.29: 13970 3.29 - 3.83: 25745 3.83 - 4.36: 30358 4.36 - 4.90: 52338 Nonbonded interactions: 124498 Sorted by model distance: nonbonded pdb=" O LEU B 253 " pdb=" OG1 THR B 257 " model vdw 2.222 2.440 nonbonded pdb=" O LEU E 253 " pdb=" OG1 THR E 257 " model vdw 2.238 2.440 nonbonded pdb=" O LEU C 268 " pdb=" OG1 THR C 272 " model vdw 2.266 2.440 nonbonded pdb=" OD1 ASP D 98 " pdb=" OG SER D 159 " model vdw 2.283 2.440 nonbonded pdb=" O VAL C 248 " pdb=" OG SER C 251 " model vdw 2.309 2.440 ... (remaining 124493 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 10 through 320 or resid 384 through 418)) selection = (chain 'D' and resid 10 through 418) } ncs_group { reference = (chain 'B' and (resid 8 through 312 or resid 419 through 447)) selection = (chain 'E' and resid 8 through 447) } ncs_group { reference = (chain 'F' and (resid 2 or resid 5 through 7)) selection = (chain 'I' and (resid 1 or resid 4 through 6)) selection = (chain 'M' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } 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 group one per residue 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: 0.610 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: 3.710 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 40.440 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 0.068 15692 Z= 0.406 Angle : 1.045 13.558 21338 Z= 0.621 Chirality : 0.059 0.559 2480 Planarity : 0.007 0.065 2588 Dihedral : 9.601 109.981 5492 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -3.20 (0.17), residues: 1791 helix: -1.44 (0.18), residues: 526 sheet: -2.38 (0.22), residues: 449 loop : -2.33 (0.19), residues: 816 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 662 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 662 average time/residue: 0.3303 time to fit residues: 302.7997 Evaluate side-chains 397 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 1.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 151 optimal weight: 0.1980 chunk 135 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN A 142 HIS A 190 GLN B 54 ASN B 267 HIS B 303 ASN C 122 HIS ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 HIS D 142 HIS D 308 ASN E 64 GLN E 90 GLN E 100 ASN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 HIS G 5 GLN G 445 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 15692 Z= 0.205 Angle : 0.640 9.074 21338 Z= 0.329 Chirality : 0.043 0.270 2480 Planarity : 0.005 0.049 2588 Dihedral : 7.759 90.930 2085 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.13 % Favored : 96.82 % Rotamer Outliers : 3.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.19), residues: 1791 helix: 0.15 (0.21), residues: 554 sheet: -1.97 (0.22), residues: 476 loop : -1.79 (0.21), residues: 761 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 433 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 37 residues processed: 468 average time/residue: 0.2787 time to fit residues: 190.7867 Evaluate side-chains 390 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 353 time to evaluate : 1.642 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1427 time to fit residues: 11.9082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 0.0970 chunk 110 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 162 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 chunk 55 optimal weight: 0.0570 chunk 130 optimal weight: 4.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 88 ASN A 142 HIS B 267 HIS C 80 GLN E 54 ASN ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 15692 Z= 0.174 Angle : 0.581 7.886 21338 Z= 0.295 Chirality : 0.042 0.255 2480 Planarity : 0.004 0.072 2588 Dihedral : 6.828 85.881 2085 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -1.24 (0.20), residues: 1791 helix: 0.83 (0.22), residues: 559 sheet: -1.59 (0.23), residues: 460 loop : -1.49 (0.22), residues: 772 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 420 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 432 average time/residue: 0.2773 time to fit residues: 177.3465 Evaluate side-chains 357 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 341 time to evaluate : 1.847 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1763 time to fit residues: 7.2726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 160 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS A 229 GLN ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.065 15692 Z= 0.432 Angle : 0.696 7.075 21338 Z= 0.353 Chirality : 0.046 0.258 2480 Planarity : 0.005 0.046 2588 Dihedral : 7.334 111.338 2085 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -1.05 (0.20), residues: 1791 helix: 1.03 (0.23), residues: 566 sheet: -1.59 (0.23), residues: 464 loop : -1.35 (0.22), residues: 761 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 346 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 44 residues processed: 376 average time/residue: 0.2590 time to fit residues: 146.0463 Evaluate side-chains 367 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 323 time to evaluate : 1.739 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.1377 time to fit residues: 13.6642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 144 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 147 optimal weight: 0.1980 chunk 119 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 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 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 157 ASN C 163 HIS E 100 ASN E 113 ASN E 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 15692 Z= 0.167 Angle : 0.577 7.358 21338 Z= 0.290 Chirality : 0.043 0.307 2480 Planarity : 0.004 0.044 2588 Dihedral : 6.555 86.809 2085 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1791 helix: 1.22 (0.23), residues: 561 sheet: -1.45 (0.23), residues: 462 loop : -1.20 (0.22), residues: 768 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 376 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 393 average time/residue: 0.2766 time to fit residues: 163.1431 Evaluate side-chains 356 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 341 time to evaluate : 1.874 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1682 time to fit residues: 6.8769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 58 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 173 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 0.3980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 15692 Z= 0.214 Angle : 0.592 8.981 21338 Z= 0.295 Chirality : 0.043 0.255 2480 Planarity : 0.004 0.044 2588 Dihedral : 6.565 95.205 2085 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1791 helix: 1.36 (0.23), residues: 563 sheet: -1.38 (0.23), residues: 463 loop : -1.11 (0.23), residues: 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 344 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 358 average time/residue: 0.2739 time to fit residues: 146.7817 Evaluate side-chains 352 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 336 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1416 time to fit residues: 6.6421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 166 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 145 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 445 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 15692 Z= 0.238 Angle : 0.600 9.942 21338 Z= 0.299 Chirality : 0.043 0.253 2480 Planarity : 0.004 0.046 2588 Dihedral : 6.606 101.440 2085 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1791 helix: 1.45 (0.23), residues: 562 sheet: -1.43 (0.22), residues: 475 loop : -1.05 (0.23), residues: 754 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 350 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 360 average time/residue: 0.2698 time to fit residues: 144.4392 Evaluate side-chains 350 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 334 time to evaluate : 1.714 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.1389 time to fit residues: 6.4191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 106 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 135 optimal weight: 1.9990 chunk 156 optimal weight: 0.4980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 15692 Z= 0.245 Angle : 0.601 8.631 21338 Z= 0.301 Chirality : 0.043 0.258 2480 Planarity : 0.004 0.047 2588 Dihedral : 6.595 101.317 2085 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1791 helix: 1.53 (0.23), residues: 559 sheet: -1.42 (0.22), residues: 475 loop : -1.04 (0.23), residues: 757 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 344 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 14 residues processed: 351 average time/residue: 0.2705 time to fit residues: 141.8397 Evaluate side-chains 345 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 331 time to evaluate : 1.814 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1471 time to fit residues: 6.2464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 165 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 49 optimal weight: 0.4980 chunk 145 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 15692 Z= 0.192 Angle : 0.585 8.175 21338 Z= 0.292 Chirality : 0.042 0.266 2480 Planarity : 0.004 0.046 2588 Dihedral : 6.428 97.302 2085 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.20), residues: 1791 helix: 1.56 (0.23), residues: 563 sheet: -1.27 (0.22), residues: 473 loop : -0.97 (0.23), residues: 755 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 345 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 347 average time/residue: 0.2775 time to fit residues: 143.2125 Evaluate side-chains 332 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 329 time to evaluate : 1.890 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1433 time to fit residues: 3.1562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 103 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 118 optimal weight: 0.0040 chunk 178 optimal weight: 0.2980 chunk 164 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 151 optimal weight: 0.0000 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 15692 Z= 0.175 Angle : 0.586 8.787 21338 Z= 0.292 Chirality : 0.042 0.284 2480 Planarity : 0.004 0.047 2588 Dihedral : 6.306 94.685 2085 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.20), residues: 1791 helix: 1.60 (0.23), residues: 562 sheet: -1.07 (0.23), residues: 469 loop : -0.94 (0.23), residues: 760 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 343 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 344 average time/residue: 0.2789 time to fit residues: 144.4530 Evaluate side-chains 328 residues out of total 1619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 324 time to evaluate : 1.766 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2267 time to fit residues: 3.8865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 43 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 GLN C 54 HIS E 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098922 restraints weight = 24724.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.101780 restraints weight = 13496.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.103669 restraints weight = 9384.832| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 15692 Z= 0.172 Angle : 0.583 8.261 21338 Z= 0.290 Chirality : 0.042 0.294 2480 Planarity : 0.004 0.047 2588 Dihedral : 6.242 94.460 2085 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.20), residues: 1791 helix: 1.65 (0.23), residues: 555 sheet: -0.93 (0.23), residues: 468 loop : -0.95 (0.23), residues: 768 =============================================================================== Job complete usr+sys time: 3505.78 seconds wall clock time: 64 minutes 36.16 seconds (3876.16 seconds total)