Starting phenix.real_space_refine on Fri Mar 15 02:46:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kak_22773/03_2024/7kak_22773.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kak_22773/03_2024/7kak_22773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kak_22773/03_2024/7kak_22773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kak_22773/03_2024/7kak_22773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kak_22773/03_2024/7kak_22773.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kak_22773/03_2024/7kak_22773.pdb" } resolution = 3.9 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= 0.004 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 6796 2.51 5 N 1789 2.21 5 O 1803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 61": "OD1" <-> "OD2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "D ARG 230": "NH1" <-> "NH2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ASP 307": "OD1" <-> "OD2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D ASP 326": "OD1" <-> "OD2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 545": "NH1" <-> "NH2" Residue "D PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 618": "OE1" <-> "OE2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E ARG 173": "NH1" <-> "NH2" Residue "F ASP 16": "OD1" <-> "OD2" Residue "F ARG 88": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 118": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10437 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3331 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 8, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 440 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 245 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3612 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 31, 'TRANS': 438} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 78 Chain: "E" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1355 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "F" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1454 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 5.67, per 1000 atoms: 0.54 Number of scatterers: 10437 At special positions: 0 Unit cell: (107.16, 125.4, 136.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 1803 8.00 N 1789 7.00 C 6796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 1.9 seconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 7 sheets defined 67.8% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 28 through 48 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 66 through 71 Processing helix chain 'A' and resid 82 through 99 removed outlier: 3.506A pdb=" N ILE A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 136 removed outlier: 3.985A pdb=" N LEU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 4.142A pdb=" N GLY A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 4.101A pdb=" N GLY A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 196 removed outlier: 4.271A pdb=" N LEU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 243 through 262 removed outlier: 3.570A pdb=" N LEU A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 314 removed outlier: 3.511A pdb=" N GLN A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 383 removed outlier: 4.271A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 removed outlier: 3.942A pdb=" N LYS A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 439 removed outlier: 3.890A pdb=" N GLU A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 418 - end of helix removed outlier: 3.979A pdb=" N ALA A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 463 removed outlier: 3.589A pdb=" N ILE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 26 Processing helix chain 'C' and resid 30 through 68 removed outlier: 3.677A pdb=" N PHE C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Proline residue: C 61 - end of helix removed outlier: 3.611A pdb=" N ALA C 68 " --> pdb=" O ASN C 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 123 removed outlier: 3.842A pdb=" N VAL B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 100 " --> pdb=" O PRO B 96 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 33 Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 56 through 68 removed outlier: 4.151A pdb=" N LEU D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 97 removed outlier: 4.204A pdb=" N ILE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 3.753A pdb=" N ILE D 196 " --> pdb=" O PRO D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 228 removed outlier: 4.578A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Proline residue: D 218 - end of helix Processing helix chain 'D' and resid 237 through 247 removed outlier: 3.700A pdb=" N ARG D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 262 removed outlier: 4.032A pdb=" N VAL D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN D 259 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.881A pdb=" N GLU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 291 removed outlier: 3.675A pdb=" N ASP D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.826A pdb=" N ILE D 306 " --> pdb=" O VAL D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 323 Processing helix chain 'D' and resid 332 through 357 removed outlier: 4.067A pdb=" N GLU D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 345 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 375 removed outlier: 3.664A pdb=" N GLN D 375 " --> pdb=" O GLN D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 387 removed outlier: 3.572A pdb=" N LEU D 385 " --> pdb=" O SER D 382 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN D 386 " --> pdb=" O PRO D 383 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU D 387 " --> pdb=" O LEU D 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 382 through 387' Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 408 through 414 Processing helix chain 'D' and resid 418 through 423 Processing helix chain 'D' and resid 431 through 443 removed outlier: 3.818A pdb=" N SER D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 36 Proline residue: E 9 - end of helix Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 71 through 104 removed outlier: 4.315A pdb=" N GLN E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 138 removed outlier: 3.652A pdb=" N GLN E 114 " --> pdb=" O ASP E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 167 removed outlier: 3.934A pdb=" N PHE E 146 " --> pdb=" O GLY E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 180 Processing helix chain 'F' and resid 31 through 56 removed outlier: 4.108A pdb=" N ASP F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 87 removed outlier: 4.604A pdb=" N SER F 72 " --> pdb=" O ASN F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 107 Processing helix chain 'F' and resid 113 through 135 removed outlier: 4.108A pdb=" N ALA F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 157 through 171 Processing helix chain 'F' and resid 172 through 187 Processing helix chain 'F' and resid 192 through 203 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 6.618A pdb=" N GLU A 19 " --> pdb=" O VAL B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211 removed outlier: 3.768A pdb=" N GLU A 210 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN D 7 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281 removed outlier: 3.548A pdb=" N TYR A 281 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 267 " --> pdb=" O TYR A 281 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.613A pdb=" N VAL A 325 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 448 through 457 removed outlier: 5.975A pdb=" N ILE D 450 " --> pdb=" O ARG D 476 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG D 476 " --> pdb=" O ILE D 450 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS D 452 " --> pdb=" O LYS D 474 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 454 " --> pdb=" O VAL D 472 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 558 through 565 removed outlier: 5.942A pdb=" N LEU D 550 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 548 " --> pdb=" O PHE D 563 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE D 549 " --> pdb=" O HIS D 604 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 617 " --> pdb=" O LEU D 603 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 13 through 15 677 hydrogen bonds defined for protein. 2016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3307 1.34 - 1.46: 2203 1.46 - 1.58: 5075 1.58 - 1.69: 0 1.69 - 1.81: 85 Bond restraints: 10670 Sorted by residual: bond pdb=" C PRO F 57 " pdb=" N PRO F 58 " ideal model delta sigma weight residual 1.330 1.357 -0.027 1.25e-02 6.40e+03 4.57e+00 bond pdb=" N PRO D 29 " pdb=" CA PRO D 29 " ideal model delta sigma weight residual 1.471 1.458 0.013 1.29e-02 6.01e+03 9.96e-01 bond pdb=" CB PRO D 536 " pdb=" CG PRO D 536 " ideal model delta sigma weight residual 1.492 1.538 -0.046 5.00e-02 4.00e+02 8.43e-01 bond pdb=" CA ILE D 361 " pdb=" CB ILE D 361 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.15e-01 bond pdb=" C LEU D 28 " pdb=" O LEU D 28 " ideal model delta sigma weight residual 1.244 1.236 0.008 1.00e-02 1.00e+04 5.80e-01 ... (remaining 10665 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.08: 387 107.08 - 113.81: 6082 113.81 - 120.54: 4344 120.54 - 127.26: 3560 127.26 - 133.99: 133 Bond angle restraints: 14506 Sorted by residual: angle pdb=" N PRO D 29 " pdb=" CA PRO D 29 " pdb=" CB PRO D 29 " ideal model delta sigma weight residual 103.44 110.15 -6.71 1.12e+00 7.97e-01 3.59e+01 angle pdb=" CA LEU D 28 " pdb=" C LEU D 28 " pdb=" N PRO D 29 " ideal model delta sigma weight residual 120.77 116.97 3.80 9.70e-01 1.06e+00 1.54e+01 angle pdb=" N SER A 289 " pdb=" CA SER A 289 " pdb=" C SER A 289 " ideal model delta sigma weight residual 111.02 114.52 -3.50 1.22e+00 6.72e-01 8.24e+00 angle pdb=" C ILE A 417 " pdb=" CA ILE A 417 " pdb=" CB ILE A 417 " ideal model delta sigma weight residual 114.00 110.53 3.47 1.31e+00 5.83e-01 7.01e+00 angle pdb=" CA LEU A 63 " pdb=" CB LEU A 63 " pdb=" CG LEU A 63 " ideal model delta sigma weight residual 116.30 125.25 -8.95 3.50e+00 8.16e-02 6.54e+00 ... (remaining 14501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5940 17.85 - 35.70: 382 35.70 - 53.56: 50 53.56 - 71.41: 5 71.41 - 89.26: 4 Dihedral angle restraints: 6381 sinusoidal: 2413 harmonic: 3968 Sorted by residual: dihedral pdb=" CB GLU A 169 " pdb=" CG GLU A 169 " pdb=" CD GLU A 169 " pdb=" OE1 GLU A 169 " ideal model delta sinusoidal sigma weight residual 0.00 89.26 -89.26 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" N PRO D 29 " pdb=" C PRO D 29 " pdb=" CA PRO D 29 " pdb=" CB PRO D 29 " ideal model delta harmonic sigma weight residual 115.10 122.79 -7.69 0 2.50e+00 1.60e-01 9.47e+00 dihedral pdb=" CA ARG E 48 " pdb=" CB ARG E 48 " pdb=" CG ARG E 48 " pdb=" CD ARG E 48 " ideal model delta sinusoidal sigma weight residual -60.00 -110.93 50.93 3 1.50e+01 4.44e-03 8.96e+00 ... (remaining 6378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1379 0.046 - 0.092: 270 0.092 - 0.138: 40 0.138 - 0.184: 0 0.184 - 0.230: 2 Chirality restraints: 1691 Sorted by residual: chirality pdb=" CA PRO D 29 " pdb=" N PRO D 29 " pdb=" C PRO D 29 " pdb=" CB PRO D 29 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE D 473 " pdb=" CA ILE D 473 " pdb=" CG1 ILE D 473 " pdb=" CG2 ILE D 473 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA THR A 83 " pdb=" N THR A 83 " pdb=" C THR A 83 " pdb=" CB THR A 83 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1688 not shown) Planarity restraints: 1816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 141 " 0.020 2.00e-02 2.50e+03 1.30e-02 4.24e+00 pdb=" CG TRP E 141 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP E 141 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP E 141 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 141 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 141 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 141 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 141 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 141 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 141 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 426 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO D 427 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 427 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 427 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 56 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO F 57 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO F 57 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 57 " -0.025 5.00e-02 4.00e+02 ... (remaining 1813 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2176 2.78 - 3.31: 10222 3.31 - 3.84: 16711 3.84 - 4.37: 16831 4.37 - 4.90: 30500 Nonbonded interactions: 76440 Sorted by model distance: nonbonded pdb=" O PHE A 198 " pdb=" OH TYR C 53 " model vdw 2.246 2.440 nonbonded pdb=" OE1 GLU A 79 " pdb=" OH TYR A 139 " model vdw 2.287 2.440 nonbonded pdb=" OD1 ASN E 155 " pdb=" NH2 ARG E 159 " model vdw 2.291 2.520 nonbonded pdb=" NH1 ARG E 159 " pdb=" O ALA F 106 " model vdw 2.293 2.520 nonbonded pdb=" O SER D 228 " pdb=" OG SER D 228 " model vdw 2.296 2.440 ... (remaining 76435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.790 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: 3.920 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 28.420 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.003 0.046 10670 Z= 0.164 Angle : 0.543 8.951 14506 Z= 0.291 Chirality : 0.037 0.230 1691 Planarity : 0.004 0.047 1816 Dihedral : 11.574 89.261 3819 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1341 helix: -0.01 (0.17), residues: 871 sheet: -2.04 (0.60), residues: 63 loop : -2.52 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 141 HIS 0.004 0.001 HIS C 59 PHE 0.011 0.001 PHE E 42 TYR 0.006 0.001 TYR E 51 ARG 0.002 0.000 ARG D 540 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8840 (tmm) cc_final: 0.7619 (mmp) REVERT: A 125 LEU cc_start: 0.9782 (tt) cc_final: 0.9554 (pp) REVERT: A 131 CYS cc_start: 0.9122 (m) cc_final: 0.8727 (m) REVERT: D 217 LEU cc_start: 0.9299 (tp) cc_final: 0.9096 (tt) REVERT: E 121 LYS cc_start: 0.9305 (mmtm) cc_final: 0.9104 (pttt) REVERT: E 162 MET cc_start: 0.9115 (tpp) cc_final: 0.8902 (tpp) REVERT: F 177 ARG cc_start: 0.9150 (mtp-110) cc_final: 0.8686 (mmp-170) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2828 time to fit residues: 56.7731 Evaluate side-chains 98 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 156 GLN A 261 GLN D 56 HIS D 61 GLN D 444 GLN D 529 GLN D 604 HIS E 95 GLN ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10670 Z= 0.386 Angle : 0.691 10.738 14506 Z= 0.341 Chirality : 0.039 0.140 1691 Planarity : 0.005 0.049 1816 Dihedral : 3.596 15.447 1474 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.80 % Allowed : 13.42 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.23), residues: 1341 helix: 1.15 (0.18), residues: 883 sheet: -1.97 (0.61), residues: 73 loop : -1.98 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 141 HIS 0.006 0.001 HIS D 534 PHE 0.027 0.002 PHE E 42 TYR 0.018 0.001 TYR F 100 ARG 0.003 0.000 ARG D 476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8944 (tmm) cc_final: 0.7528 (mmp) REVERT: A 131 CYS cc_start: 0.9206 (m) cc_final: 0.8711 (m) REVERT: D 252 MET cc_start: 0.8879 (ppp) cc_final: 0.8514 (ppp) REVERT: E 162 MET cc_start: 0.9208 (tpp) cc_final: 0.8989 (tpp) REVERT: F 100 TYR cc_start: 0.9050 (t80) cc_final: 0.8771 (t80) outliers start: 19 outliers final: 13 residues processed: 109 average time/residue: 0.2260 time to fit residues: 35.3862 Evaluate side-chains 98 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 333 ASN Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 0.0980 chunk 102 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10670 Z= 0.195 Angle : 0.591 10.739 14506 Z= 0.283 Chirality : 0.037 0.180 1691 Planarity : 0.004 0.047 1816 Dihedral : 3.423 16.614 1474 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.51 % Allowed : 17.86 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.24), residues: 1341 helix: 1.59 (0.18), residues: 881 sheet: -1.67 (0.63), residues: 73 loop : -1.72 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 141 HIS 0.003 0.001 HIS C 59 PHE 0.020 0.001 PHE D 563 TYR 0.008 0.001 TYR A 457 ARG 0.007 0.000 ARG F 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8967 (tmm) cc_final: 0.7612 (mmp) REVERT: A 131 CYS cc_start: 0.9184 (m) cc_final: 0.8671 (m) REVERT: A 401 MET cc_start: 0.7722 (pmm) cc_final: 0.7469 (pmm) REVERT: E 162 MET cc_start: 0.9154 (tpp) cc_final: 0.8873 (tpp) REVERT: F 137 MET cc_start: 0.7428 (mpp) cc_final: 0.7200 (mpp) outliers start: 16 outliers final: 10 residues processed: 103 average time/residue: 0.1803 time to fit residues: 28.5737 Evaluate side-chains 98 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10670 Z= 0.311 Angle : 0.637 10.782 14506 Z= 0.311 Chirality : 0.038 0.164 1691 Planarity : 0.004 0.045 1816 Dihedral : 3.571 15.581 1474 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.12 % Allowed : 18.53 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1341 helix: 1.77 (0.18), residues: 887 sheet: -1.42 (0.65), residues: 73 loop : -1.58 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 141 HIS 0.006 0.001 HIS D 534 PHE 0.019 0.002 PHE E 42 TYR 0.008 0.001 TYR D 610 ARG 0.004 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 87 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9019 (tmm) cc_final: 0.7600 (mmp) REVERT: A 68 MET cc_start: 0.8889 (tmm) cc_final: 0.8318 (tmm) REVERT: A 69 MET cc_start: 0.9251 (tpp) cc_final: 0.8602 (tpp) REVERT: A 131 CYS cc_start: 0.9207 (m) cc_final: 0.8716 (m) REVERT: E 162 MET cc_start: 0.9147 (tpp) cc_final: 0.8845 (tpp) REVERT: F 133 MET cc_start: 0.9537 (OUTLIER) cc_final: 0.9317 (mtt) outliers start: 33 outliers final: 17 residues processed: 113 average time/residue: 0.1841 time to fit residues: 31.7921 Evaluate side-chains 102 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 133 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 90 optimal weight: 0.0770 chunk 0 optimal weight: 30.0000 chunk 66 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 104 GLN F 30 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10670 Z= 0.163 Angle : 0.580 10.731 14506 Z= 0.274 Chirality : 0.037 0.177 1691 Planarity : 0.004 0.049 1816 Dihedral : 3.412 16.748 1474 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.70 % Allowed : 20.51 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.24), residues: 1341 helix: 1.95 (0.18), residues: 885 sheet: -1.26 (0.66), residues: 75 loop : -1.46 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 176 HIS 0.003 0.001 HIS F 132 PHE 0.017 0.001 PHE D 563 TYR 0.007 0.001 TYR A 114 ARG 0.003 0.000 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.8996 (tmm) cc_final: 0.7576 (mmp) REVERT: A 131 CYS cc_start: 0.9196 (m) cc_final: 0.8694 (m) REVERT: D 588 MET cc_start: 0.8373 (tpt) cc_final: 0.8112 (mmm) REVERT: E 23 PHE cc_start: 0.8974 (t80) cc_final: 0.8762 (t80) REVERT: E 162 MET cc_start: 0.9090 (tpp) cc_final: 0.8756 (tpp) REVERT: F 133 MET cc_start: 0.9525 (OUTLIER) cc_final: 0.9279 (mtt) outliers start: 18 outliers final: 12 residues processed: 106 average time/residue: 0.1977 time to fit residues: 31.7011 Evaluate side-chains 98 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 85 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 133 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10670 Z= 0.166 Angle : 0.590 10.789 14506 Z= 0.275 Chirality : 0.037 0.182 1691 Planarity : 0.004 0.045 1816 Dihedral : 3.345 18.475 1474 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.70 % Allowed : 21.74 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1341 helix: 2.00 (0.18), residues: 882 sheet: -1.14 (0.67), residues: 75 loop : -1.40 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 160 HIS 0.003 0.001 HIS D 534 PHE 0.013 0.001 PHE D 563 TYR 0.007 0.001 TYR A 114 ARG 0.002 0.000 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9004 (tmm) cc_final: 0.7476 (mmp) REVERT: A 131 CYS cc_start: 0.9199 (m) cc_final: 0.8702 (m) REVERT: D 252 MET cc_start: 0.8718 (ppp) cc_final: 0.8432 (ppp) REVERT: E 23 PHE cc_start: 0.8913 (t80) cc_final: 0.8697 (t80) REVERT: E 162 MET cc_start: 0.9089 (tpp) cc_final: 0.8747 (tpp) REVERT: F 121 LEU cc_start: 0.9508 (mt) cc_final: 0.9175 (mt) REVERT: F 133 MET cc_start: 0.9505 (OUTLIER) cc_final: 0.9242 (mtt) outliers start: 18 outliers final: 13 residues processed: 107 average time/residue: 0.1930 time to fit residues: 31.1143 Evaluate side-chains 102 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 133 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10670 Z= 0.151 Angle : 0.595 13.590 14506 Z= 0.275 Chirality : 0.037 0.191 1691 Planarity : 0.004 0.047 1816 Dihedral : 3.282 19.373 1474 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.80 % Allowed : 22.59 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1341 helix: 2.10 (0.18), residues: 888 sheet: -1.15 (0.65), residues: 75 loop : -1.33 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 160 HIS 0.002 0.000 HIS D 534 PHE 0.013 0.001 PHE D 15 TYR 0.008 0.001 TYR E 158 ARG 0.003 0.000 ARG E 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9005 (tmm) cc_final: 0.7469 (mmp) REVERT: A 78 MET cc_start: 0.7953 (mmm) cc_final: 0.7533 (tpp) REVERT: A 131 CYS cc_start: 0.9203 (m) cc_final: 0.8697 (m) REVERT: D 252 MET cc_start: 0.8724 (ppp) cc_final: 0.8398 (ppp) REVERT: D 588 MET cc_start: 0.8259 (tpt) cc_final: 0.7935 (tpt) REVERT: D 608 ASP cc_start: 0.9318 (OUTLIER) cc_final: 0.9002 (p0) REVERT: E 23 PHE cc_start: 0.8885 (t80) cc_final: 0.8661 (t80) REVERT: E 162 MET cc_start: 0.9095 (tpp) cc_final: 0.8640 (tpp) REVERT: F 121 LEU cc_start: 0.9504 (mt) cc_final: 0.9175 (mt) REVERT: F 133 MET cc_start: 0.9509 (OUTLIER) cc_final: 0.9264 (mtt) REVERT: F 137 MET cc_start: 0.7271 (mpp) cc_final: 0.6684 (pmm) outliers start: 19 outliers final: 13 residues processed: 113 average time/residue: 0.2082 time to fit residues: 35.6429 Evaluate side-chains 107 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 608 ASP Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 133 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 0.0370 chunk 82 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 12 optimal weight: 0.1980 chunk 102 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 overall best weight: 3.8464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10670 Z= 0.301 Angle : 0.653 11.956 14506 Z= 0.311 Chirality : 0.038 0.175 1691 Planarity : 0.004 0.044 1816 Dihedral : 3.480 19.645 1474 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.98 % Allowed : 22.97 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.24), residues: 1341 helix: 2.20 (0.18), residues: 891 sheet: -1.07 (0.65), residues: 75 loop : -1.23 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 141 HIS 0.005 0.001 HIS C 59 PHE 0.015 0.001 PHE E 42 TYR 0.008 0.001 TYR D 321 ARG 0.003 0.000 ARG D 587 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9038 (tmm) cc_final: 0.7545 (mmp) REVERT: A 131 CYS cc_start: 0.9229 (m) cc_final: 0.8747 (m) REVERT: D 252 MET cc_start: 0.8733 (ppp) cc_final: 0.8405 (ppp) REVERT: D 588 MET cc_start: 0.8181 (tpt) cc_final: 0.7900 (tpt) REVERT: D 608 ASP cc_start: 0.9434 (OUTLIER) cc_final: 0.9117 (p0) REVERT: E 23 PHE cc_start: 0.8963 (t80) cc_final: 0.8727 (t80) REVERT: E 162 MET cc_start: 0.9182 (tpp) cc_final: 0.8911 (tpp) REVERT: F 133 MET cc_start: 0.9509 (OUTLIER) cc_final: 0.9269 (mtt) outliers start: 21 outliers final: 14 residues processed: 103 average time/residue: 0.1784 time to fit residues: 28.4348 Evaluate side-chains 102 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 608 ASP Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 133 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 8.9990 chunk 121 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 0.0270 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10670 Z= 0.155 Angle : 0.617 12.694 14506 Z= 0.284 Chirality : 0.038 0.321 1691 Planarity : 0.004 0.049 1816 Dihedral : 3.345 20.881 1474 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.32 % Allowed : 23.16 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.24), residues: 1341 helix: 2.29 (0.18), residues: 884 sheet: -1.05 (0.65), residues: 75 loop : -1.16 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 141 HIS 0.003 0.000 HIS D 534 PHE 0.022 0.001 PHE B 106 TYR 0.008 0.001 TYR A 114 ARG 0.003 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9000 (tmm) cc_final: 0.7423 (mmp) REVERT: A 78 MET cc_start: 0.7928 (mmm) cc_final: 0.7544 (tpp) REVERT: A 131 CYS cc_start: 0.9219 (m) cc_final: 0.8734 (m) REVERT: D 252 MET cc_start: 0.8741 (ppp) cc_final: 0.8389 (ppp) REVERT: D 588 MET cc_start: 0.8145 (tpt) cc_final: 0.7830 (tpt) REVERT: D 608 ASP cc_start: 0.9327 (OUTLIER) cc_final: 0.9024 (p0) REVERT: E 23 PHE cc_start: 0.8857 (t80) cc_final: 0.8642 (t80) REVERT: E 162 MET cc_start: 0.9091 (tpp) cc_final: 0.8725 (tpp) REVERT: F 121 LEU cc_start: 0.9522 (mt) cc_final: 0.9160 (mt) REVERT: F 133 MET cc_start: 0.9524 (OUTLIER) cc_final: 0.9287 (mtt) REVERT: F 137 MET cc_start: 0.7402 (mpp) cc_final: 0.7142 (pmm) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.1751 time to fit residues: 27.6389 Evaluate side-chains 102 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 608 ASP Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 133 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 65 optimal weight: 0.0870 chunk 85 optimal weight: 10.0000 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10670 Z= 0.186 Angle : 0.626 12.187 14506 Z= 0.287 Chirality : 0.037 0.255 1691 Planarity : 0.004 0.046 1816 Dihedral : 3.310 21.501 1474 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.13 % Allowed : 23.44 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.24), residues: 1341 helix: 2.36 (0.18), residues: 885 sheet: -0.98 (0.64), residues: 75 loop : -1.11 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 141 HIS 0.003 0.001 HIS D 534 PHE 0.012 0.001 PHE D 15 TYR 0.009 0.001 TYR D 412 ARG 0.002 0.000 ARG F 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9010 (tmm) cc_final: 0.7443 (mmp) REVERT: A 78 MET cc_start: 0.8004 (mmm) cc_final: 0.7586 (tpp) REVERT: A 131 CYS cc_start: 0.9235 (m) cc_final: 0.8750 (m) REVERT: A 401 MET cc_start: 0.7480 (pmm) cc_final: 0.6998 (ptp) REVERT: D 252 MET cc_start: 0.8742 (ppp) cc_final: 0.8380 (ppp) REVERT: D 588 MET cc_start: 0.8142 (tpt) cc_final: 0.7866 (tpt) REVERT: D 608 ASP cc_start: 0.9365 (OUTLIER) cc_final: 0.9056 (p0) REVERT: E 23 PHE cc_start: 0.8873 (t80) cc_final: 0.8665 (t80) REVERT: E 162 MET cc_start: 0.9135 (tpp) cc_final: 0.8575 (tpp) REVERT: F 121 LEU cc_start: 0.9565 (mt) cc_final: 0.9235 (mt) REVERT: F 133 MET cc_start: 0.9483 (OUTLIER) cc_final: 0.9247 (mtt) REVERT: F 137 MET cc_start: 0.7451 (mpp) cc_final: 0.7177 (pmm) outliers start: 12 outliers final: 10 residues processed: 99 average time/residue: 0.1664 time to fit residues: 25.7774 Evaluate side-chains 100 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 237 TYR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 344 TYR Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 473 ILE Chi-restraints excluded: chain D residue 608 ASP Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 133 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 98 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.051786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.041373 restraints weight = 73771.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.042427 restraints weight = 40129.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.043113 restraints weight = 26825.399| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10670 Z= 0.179 Angle : 0.618 12.245 14506 Z= 0.284 Chirality : 0.037 0.228 1691 Planarity : 0.004 0.046 1816 Dihedral : 3.314 21.762 1474 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.23 % Allowed : 23.44 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.24), residues: 1341 helix: 2.39 (0.18), residues: 884 sheet: -0.94 (0.64), residues: 75 loop : -1.06 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 141 HIS 0.003 0.001 HIS D 534 PHE 0.013 0.001 PHE D 15 TYR 0.007 0.001 TYR A 114 ARG 0.002 0.000 ARG F 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1712.33 seconds wall clock time: 31 minutes 57.15 seconds (1917.15 seconds total)