Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 18:34:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpa_16147/07_2023/8bpa_16147.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpa_16147/07_2023/8bpa_16147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpa_16147/07_2023/8bpa_16147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpa_16147/07_2023/8bpa_16147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpa_16147/07_2023/8bpa_16147.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpa_16147/07_2023/8bpa_16147.pdb" } resolution = 3.7 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= 0.002 sd= 0.037 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 5 6.06 5 S 71 5.16 5 C 6618 2.51 5 N 1791 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "A ASP 463": "OD1" <-> "OD2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "A TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 740": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "A ASP 821": "OD1" <-> "OD2" Residue "A TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 838": "OD1" <-> "OD2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "A PHE 852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 156": "OD1" <-> "OD2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B ASP 214": "OD1" <-> "OD2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B ASP 235": "OD1" <-> "OD2" Residue "B TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B ASP 270": "OD1" <-> "OD2" Residue "B TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D ASP 332": "OD1" <-> "OD2" Residue "D PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 10393 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4403 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 518} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 368, 2956 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 351} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1692 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 191} Chain breaks: 3 Chain: "D" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 153} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8431 SG CYS C 289 39.856 57.677 45.495 1.00125.91 S ATOM 8457 SG CYS C 292 37.187 56.181 43.096 1.00124.81 S ATOM 8640 SG CYS C 315 40.824 55.364 42.492 1.00117.18 S ATOM 8315 SG CYS C 274 39.422 44.839 47.811 1.00110.14 S ATOM 8339 SG CYS C 277 40.602 41.173 47.436 1.00113.17 S ATOM 8523 SG CYS C 300 42.904 43.509 48.758 1.00 86.93 S ATOM 7590 SG CYS C 71 48.790 94.141 75.277 1.00204.68 S ATOM 7614 SG CYS C 74 45.627 93.112 73.314 1.00205.36 S ATOM 7806 SG CYS C 99 47.990 95.411 71.662 1.00187.58 S ATOM 7833 SG CYS C 102 46.167 96.786 74.406 1.00184.08 S ATOM 7508 SG CYS C 59 50.564 85.329 66.806 1.00204.38 S ATOM 7528 SG CYS C 62 51.157 83.018 63.861 1.00188.96 S ATOM 7675 SG CYS C 82 53.191 86.280 64.136 1.00181.00 S Time building chain proxies: 5.54, per 1000 atoms: 0.53 Number of scatterers: 10393 At special positions: 0 Unit cell: (122.094, 124.146, 112.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 Ca 2 19.99 S 71 16.00 O 1906 8.00 N 1791 7.00 C 6618 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: 4.61 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 179 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 318 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 292 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 315 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 289 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" ND1 HIS C 297 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 300 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 277 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 274 " pdb=" ZN C1103 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 99 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 102 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 74 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 71 " pdb=" ZN C1104 " pdb="ZN ZN C1104 " - pdb=" ND1 HIS C 79 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 62 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 59 " pdb="ZN ZN C1104 " - pdb=" SG CYS C 82 " Number of angles added : 15 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 5 sheets defined 59.2% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 304 through 319 Processing helix chain 'A' and resid 320 through 336 removed outlier: 3.583A pdb=" N TYR A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 417 through 424 removed outlier: 3.594A pdb=" N LEU A 424 " --> pdb=" O CYS A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 484 removed outlier: 3.760A pdb=" N GLU A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 486 No H-bonds generated for 'chain 'A' and resid 485 through 486' Processing helix chain 'A' and resid 487 through 494 removed outlier: 5.005A pdb=" N GLU A 492 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 519 through 530 removed outlier: 3.880A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 561 removed outlier: 3.560A pdb=" N ALA A 534 " --> pdb=" O ASN A 530 " (cutoff:3.500A) Proline residue: A 536 - end of helix Processing helix chain 'A' and resid 567 through 573 removed outlier: 3.630A pdb=" N ASP A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 587 removed outlier: 4.126A pdb=" N GLN A 581 " --> pdb=" O VAL A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 610 removed outlier: 3.909A pdb=" N ILE A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 Processing helix chain 'A' and resid 648 through 667 removed outlier: 4.171A pdb=" N VAL A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Proline residue: A 664 - end of helix Processing helix chain 'A' and resid 746 through 786 removed outlier: 3.918A pdb=" N LEU A 786 " --> pdb=" O GLU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 removed outlier: 3.548A pdb=" N ARG A 792 " --> pdb=" O GLU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 829 removed outlier: 4.797A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Proline residue: A 817 - end of helix Processing helix chain 'A' and resid 832 through 845 Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.889A pdb=" N TYR A 849 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A 850 " --> pdb=" O HIS A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 871 Processing helix chain 'A' and resid 871 through 887 removed outlier: 3.671A pdb=" N LEU A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 916 removed outlier: 5.379A pdb=" N ALA A 902 " --> pdb=" O CYS A 898 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ARG A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 81 through 87 removed outlier: 3.721A pdb=" N MET B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 87 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 106 through 127 removed outlier: 3.734A pdb=" N SER B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.740A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'B' and resid 234 through 253 Proline residue: B 244 - end of helix Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.922A pdb=" N SER B 266 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 291 removed outlier: 3.982A pdb=" N CYS B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 286 " --> pdb=" O HIS B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 321 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.903A pdb=" N GLY B 339 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 373 removed outlier: 3.787A pdb=" N MET B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 28 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 206 through 220 Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 320 through 325 Processing helix chain 'C' and resid 330 through 342 removed outlier: 3.509A pdb=" N ARG C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 360 removed outlier: 3.583A pdb=" N LYS C 360 " --> pdb=" O ASN C 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 216 removed outlier: 3.975A pdb=" N VAL D 208 " --> pdb=" O LYS D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.914A pdb=" N SER D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 267 removed outlier: 3.995A pdb=" N GLU D 255 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 277 through 288 Processing helix chain 'D' and resid 299 through 313 removed outlier: 3.859A pdb=" N LEU D 303 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG D 304 " --> pdb=" O PRO D 300 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 319 through 340 Processing helix chain 'D' and resid 340 through 345 Processing helix chain 'D' and resid 354 through 362 Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397 removed outlier: 3.706A pdb=" N TYR A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 620 through 624 removed outlier: 3.639A pdb=" N LEU A 926 " --> pdb=" O ILE A 933 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS A 920 " --> pdb=" O LEU A 939 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL A 739 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55 removed outlier: 6.576A pdb=" N TYR B 14 " --> pdb=" O TYR B 55 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N CYS B 13 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA B 133 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 172 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLN B 261 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE B 174 " --> pdb=" O GLN B 261 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET B 195 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AA5, first strand: chain 'C' and resid 287 through 288 532 hydrogen bonds defined for protein. 1548 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: 2.87 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2411 1.33 - 1.45: 2238 1.45 - 1.57: 5872 1.57 - 1.69: 2 1.69 - 1.81: 104 Bond restraints: 10627 Sorted by residual: bond pdb=" CB PRO A 521 " pdb=" CG PRO A 521 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.03e+00 bond pdb=" CG PRO B 102 " pdb=" CD PRO B 102 " ideal model delta sigma weight residual 1.503 1.562 -0.059 3.40e-02 8.65e+02 3.03e+00 bond pdb=" CB PRO B 102 " pdb=" CG PRO B 102 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.94e+00 bond pdb=" CG PRO A 521 " pdb=" CD PRO A 521 " ideal model delta sigma weight residual 1.503 1.448 0.055 3.40e-02 8.65e+02 2.61e+00 bond pdb=" CB PRO C 316 " pdb=" CG PRO C 316 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.40e+00 ... (remaining 10622 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.45: 225 105.45 - 112.64: 5313 112.64 - 119.82: 3899 119.82 - 127.01: 4791 127.01 - 134.20: 124 Bond angle restraints: 14352 Sorted by residual: angle pdb=" CA PRO A 521 " pdb=" N PRO A 521 " pdb=" CD PRO A 521 " ideal model delta sigma weight residual 112.00 102.42 9.58 1.40e+00 5.10e-01 4.68e+01 angle pdb=" CA GLU A 562 " pdb=" CB GLU A 562 " pdb=" CG GLU A 562 " ideal model delta sigma weight residual 114.10 124.56 -10.46 2.00e+00 2.50e-01 2.73e+01 angle pdb=" C LYS C 32 " pdb=" CA LYS C 32 " pdb=" CB LYS C 32 " ideal model delta sigma weight residual 115.79 110.05 5.74 1.19e+00 7.06e-01 2.33e+01 angle pdb=" CA LYS A 885 " pdb=" CB LYS A 885 " pdb=" CG LYS A 885 " ideal model delta sigma weight residual 114.10 122.28 -8.18 2.00e+00 2.50e-01 1.67e+01 angle pdb=" CA GLU A 879 " pdb=" CB GLU A 879 " pdb=" CG GLU A 879 " ideal model delta sigma weight residual 114.10 121.86 -7.76 2.00e+00 2.50e-01 1.50e+01 ... (remaining 14347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5369 17.86 - 35.72: 779 35.72 - 53.58: 245 53.58 - 71.44: 40 71.44 - 89.29: 16 Dihedral angle restraints: 6449 sinusoidal: 2681 harmonic: 3768 Sorted by residual: dihedral pdb=" CA THR B 305 " pdb=" C THR B 305 " pdb=" N ILE B 306 " pdb=" CA ILE B 306 " ideal model delta harmonic sigma weight residual -180.00 -151.39 -28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ARG A 402 " pdb=" C ARG A 402 " pdb=" N ALA A 403 " pdb=" CA ALA A 403 " ideal model delta harmonic sigma weight residual -180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA MET A 934 " pdb=" C MET A 934 " pdb=" N THR A 935 " pdb=" CA THR A 935 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 6446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1009 0.041 - 0.081: 398 0.081 - 0.122: 108 0.122 - 0.163: 16 0.163 - 0.203: 3 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CB VAL A 923 " pdb=" CA VAL A 923 " pdb=" CG1 VAL A 923 " pdb=" CG2 VAL A 923 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA PRO A 521 " pdb=" N PRO A 521 " pdb=" C PRO A 521 " pdb=" CB PRO A 521 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.23e-01 chirality pdb=" CG LEU B 212 " pdb=" CB LEU B 212 " pdb=" CD1 LEU B 212 " pdb=" CD2 LEU B 212 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 1531 not shown) Planarity restraints: 1862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.067 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A 521 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 315 " -0.047 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO C 316 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 316 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 316 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 562 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C GLU A 562 " 0.046 2.00e-02 2.50e+03 pdb=" O GLU A 562 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 563 " -0.015 2.00e-02 2.50e+03 ... (remaining 1859 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 282 2.68 - 3.24: 10701 3.24 - 3.79: 17009 3.79 - 4.35: 21650 4.35 - 4.90: 34359 Nonbonded interactions: 84001 Sorted by model distance: nonbonded pdb=" O HIS B 179 " pdb="CA CA B 502 " model vdw 2.127 2.510 nonbonded pdb=" OD2 ASP B 265 " pdb="ZN ZN B 501 " model vdw 2.141 2.230 nonbonded pdb=" OG1 THR C 330 " pdb=" OD1 ASN C 333 " model vdw 2.154 2.440 nonbonded pdb=" OD1 ASP B 175 " pdb="CA CA B 502 " model vdw 2.172 2.510 nonbonded pdb=" N GLN A 835 " pdb=" OE1 GLN A 835 " model vdw 2.194 2.520 ... (remaining 83996 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=0.00 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.100 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.870 Find NCS groups from input model: 0.290 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 10627 Z= 0.307 Angle : 0.850 11.687 14352 Z= 0.446 Chirality : 0.046 0.203 1534 Planarity : 0.006 0.095 1862 Dihedral : 18.501 89.294 4015 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.00 (0.24), residues: 1260 helix: 0.74 (0.20), residues: 672 sheet: -0.57 (0.60), residues: 77 loop : -0.81 (0.28), residues: 511 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 349 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 352 average time/residue: 0.2729 time to fit residues: 127.3642 Evaluate side-chains 335 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 330 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1058 time to fit residues: 2.7422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS A 859 GLN ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN A B 308 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 10627 Z= 0.266 Angle : 0.688 9.814 14352 Z= 0.352 Chirality : 0.044 0.254 1534 Planarity : 0.005 0.079 1862 Dihedral : 4.697 25.228 1408 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 4.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.10 (0.24), residues: 1260 helix: 0.91 (0.20), residues: 678 sheet: -0.54 (0.59), residues: 75 loop : -0.94 (0.28), residues: 507 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 351 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 26 residues processed: 382 average time/residue: 0.2866 time to fit residues: 147.1749 Evaluate side-chains 350 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 324 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.0990 time to fit residues: 6.4778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 168 HIS B 240 GLN A B 282 HIS B 308 ASN C 100 HIS ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.110 10627 Z= 0.372 Angle : 0.781 11.207 14352 Z= 0.403 Chirality : 0.048 0.430 1534 Planarity : 0.005 0.065 1862 Dihedral : 5.053 27.165 1408 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: -0.30 (0.23), residues: 1260 helix: 0.56 (0.19), residues: 681 sheet: -0.85 (0.56), residues: 73 loop : -1.07 (0.28), residues: 506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 342 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 19 residues processed: 365 average time/residue: 0.2867 time to fit residues: 138.6744 Evaluate side-chains 355 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 336 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1178 time to fit residues: 5.5957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 45 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN A ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 10627 Z= 0.215 Angle : 0.695 11.271 14352 Z= 0.347 Chirality : 0.043 0.337 1534 Planarity : 0.005 0.046 1862 Dihedral : 4.699 25.712 1408 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 3.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.09 (0.24), residues: 1260 helix: 0.94 (0.20), residues: 677 sheet: -0.72 (0.54), residues: 78 loop : -0.96 (0.29), residues: 505 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 339 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 15 residues processed: 359 average time/residue: 0.2644 time to fit residues: 128.6739 Evaluate side-chains 332 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 317 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1977 time to fit residues: 5.9511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.0770 chunk 109 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS A 859 GLN ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS ** B 91 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN A ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 10627 Z= 0.229 Angle : 0.704 13.063 14352 Z= 0.348 Chirality : 0.043 0.343 1534 Planarity : 0.005 0.046 1862 Dihedral : 4.609 25.464 1408 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.24 (0.24), residues: 1260 helix: 1.10 (0.20), residues: 677 sheet: -0.56 (0.56), residues: 78 loop : -0.98 (0.29), residues: 505 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 337 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 344 average time/residue: 0.2858 time to fit residues: 131.3415 Evaluate side-chains 327 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 317 time to evaluate : 1.207 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1503 time to fit residues: 4.0870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS A 859 GLN ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 10627 Z= 0.238 Angle : 0.709 11.707 14352 Z= 0.354 Chirality : 0.045 0.395 1534 Planarity : 0.005 0.052 1862 Dihedral : 4.642 26.095 1408 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.17 (0.24), residues: 1260 helix: 1.08 (0.20), residues: 672 sheet: -0.58 (0.56), residues: 78 loop : -1.06 (0.28), residues: 510 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 337 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 349 average time/residue: 0.2761 time to fit residues: 128.9465 Evaluate side-chains 340 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 327 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1070 time to fit residues: 4.1868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 0.0040 chunk 121 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 10627 Z= 0.207 Angle : 0.696 13.237 14352 Z= 0.344 Chirality : 0.043 0.358 1534 Planarity : 0.005 0.053 1862 Dihedral : 4.504 24.994 1408 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.31 (0.24), residues: 1260 helix: 1.22 (0.20), residues: 669 sheet: -0.36 (0.58), residues: 77 loop : -1.05 (0.28), residues: 514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 334 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 345 average time/residue: 0.2644 time to fit residues: 122.0640 Evaluate side-chains 333 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 322 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1116 time to fit residues: 3.8861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS A 771 GLN A 859 GLN ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN B 34 HIS ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 10627 Z= 0.243 Angle : 0.734 12.796 14352 Z= 0.363 Chirality : 0.044 0.357 1534 Planarity : 0.005 0.070 1862 Dihedral : 4.633 26.053 1408 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.20 (0.24), residues: 1260 helix: 1.10 (0.20), residues: 668 sheet: -0.53 (0.58), residues: 78 loop : -1.02 (0.29), residues: 514 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 334 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 338 average time/residue: 0.2609 time to fit residues: 119.7646 Evaluate side-chains 335 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 325 time to evaluate : 1.286 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1148 time to fit residues: 3.7619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 HIS ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 10627 Z= 0.241 Angle : 0.744 13.072 14352 Z= 0.369 Chirality : 0.045 0.364 1534 Planarity : 0.005 0.070 1862 Dihedral : 4.749 25.941 1408 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.12 (0.24), residues: 1260 helix: 1.03 (0.20), residues: 669 sheet: -0.49 (0.58), residues: 77 loop : -1.08 (0.28), residues: 514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 324 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 329 average time/residue: 0.2571 time to fit residues: 115.4358 Evaluate side-chains 329 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 319 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1080 time to fit residues: 3.5594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 GLN A 607 HIS A 660 HIS A 773 GLN A 859 GLN ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 282 HIS ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 10627 Z= 0.223 Angle : 0.767 13.115 14352 Z= 0.380 Chirality : 0.045 0.369 1534 Planarity : 0.005 0.068 1862 Dihedral : 4.725 25.461 1408 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.07 (0.24), residues: 1260 helix: 0.94 (0.20), residues: 669 sheet: -0.45 (0.59), residues: 77 loop : -1.04 (0.28), residues: 514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 326 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 329 average time/residue: 0.2647 time to fit residues: 117.2331 Evaluate side-chains 317 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 315 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1153 time to fit residues: 2.0199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 41 optimal weight: 0.0870 chunk 102 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 HIS A 773 GLN ** A 883 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.165988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.139084 restraints weight = 20275.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.143623 restraints weight = 11143.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.146570 restraints weight = 7128.304| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4034 r_free = 0.4034 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 10627 Z= 0.212 Angle : 0.767 13.459 14352 Z= 0.379 Chirality : 0.044 0.372 1534 Planarity : 0.005 0.064 1862 Dihedral : 4.613 22.555 1408 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % 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: 0.14 (0.24), residues: 1260 helix: 1.01 (0.20), residues: 662 sheet: -0.39 (0.60), residues: 77 loop : -0.99 (0.28), residues: 521 =============================================================================== Job complete usr+sys time: 2851.52 seconds wall clock time: 52 minutes 13.23 seconds (3133.23 seconds total)