Starting phenix.real_space_refine on Sun Jul 21 06:12:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytj_34090/07_2024/7ytj_34090.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytj_34090/07_2024/7ytj_34090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytj_34090/07_2024/7ytj_34090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytj_34090/07_2024/7ytj_34090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytj_34090/07_2024/7ytj_34090.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ytj_34090/07_2024/7ytj_34090.cif" } resolution = 3.0 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= 0.002 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 22 5.49 5 S 34 5.16 5 C 8474 2.51 5 N 2194 2.21 5 O 2413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 24": "OD1" <-> "OD2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D ASP 235": "OD1" <-> "OD2" Residue "D ASP 244": "OD1" <-> "OD2" Residue "D GLU 380": "OE1" <-> "OE2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D ASP 473": "OD1" <-> "OD2" Residue "D PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 180": "OE1" <-> "OE2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 188": "OE1" <-> "OE2" Residue "E TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "E ASP 322": "OD1" <-> "OD2" Residue "E ASP 478": "OD1" <-> "OD2" Residue "E ASP 481": "OD1" <-> "OD2" Residue "E ASP 496": "OD1" <-> "OD2" Residue "E GLU 550": "OE1" <-> "OE2" Residue "E PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 585": "OD1" <-> "OD2" Residue "E GLU 733": "OE1" <-> "OE2" Residue "E PHE 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13137 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 4940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4940 Classifications: {'peptide': 601} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 574} Chain breaks: 2 Chain: "A" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 941 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "B" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 811 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 811 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "E" Number of atoms: 5408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5408 Classifications: {'peptide': 650} Link IDs: {'PTRANS': 28, 'TRANS': 621} Chain breaks: 3 Chain: "D" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 172 Unusual residues: {'IHP': 3, 'PC1': 1, 'PO4': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.08, per 1000 atoms: 0.54 Number of scatterers: 13137 At special positions: 0 Unit cell: (111.28, 93.09, 169.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 22 15.00 O 2413 8.00 N 2194 7.00 C 8474 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: 5.48 Conformation dependent library (CDL) restraints added in 2.5 seconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 63.3% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 42 through 88 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 95 through 139 removed outlier: 3.830A pdb=" N ASP D 99 " --> pdb=" O PRO D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 Processing helix chain 'D' and resid 161 through 180 Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 208 through 218 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 302 through 310 removed outlier: 4.488A pdb=" N ASN D 306 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASP D 307 " --> pdb=" O ARG D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 319 Processing helix chain 'D' and resid 319 through 326 removed outlier: 3.564A pdb=" N ARG D 323 " --> pdb=" O PHE D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 351 Processing helix chain 'D' and resid 439 through 447 Processing helix chain 'D' and resid 458 through 468 Processing helix chain 'D' and resid 469 through 472 Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.543A pdb=" N MET D 482 " --> pdb=" O LEU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 652 removed outlier: 3.951A pdb=" N GLU D 629 " --> pdb=" O TYR D 625 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 632 " --> pdb=" O THR D 628 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE D 638 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 687 removed outlier: 4.204A pdb=" N GLY D 660 " --> pdb=" O THR D 656 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY D 663 " --> pdb=" O ILE D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 690 No H-bonds generated for 'chain 'D' and resid 688 through 690' Processing helix chain 'D' and resid 698 through 724 Processing helix chain 'A' and resid 56 through 88 removed outlier: 4.460A pdb=" N PHE A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 124 removed outlier: 4.147A pdb=" N GLY A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 156 Processing helix chain 'B' and resid 56 through 88 removed outlier: 3.634A pdb=" N PHE B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 124 removed outlier: 3.661A pdb=" N SER B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 156 removed outlier: 3.874A pdb=" N THR B 136 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 88 removed outlier: 3.533A pdb=" N PHE C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 124 Processing helix chain 'C' and resid 133 through 156 Processing helix chain 'E' and resid 32 through 39 Processing helix chain 'E' and resid 41 through 48 removed outlier: 5.267A pdb=" N ASP E 46 " --> pdb=" O PRO E 43 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR E 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 64 removed outlier: 4.430A pdb=" N SER E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL E 62 " --> pdb=" O LEU E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 112 Processing helix chain 'E' and resid 116 through 122 Processing helix chain 'E' and resid 124 through 164 Processing helix chain 'E' and resid 170 through 180 removed outlier: 3.667A pdb=" N LEU E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 207 removed outlier: 3.551A pdb=" N TYR E 194 " --> pdb=" O SER E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 255 removed outlier: 4.427A pdb=" N MET E 247 " --> pdb=" O ASP E 243 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU E 248 " --> pdb=" O ASP E 244 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 343 Processing helix chain 'E' and resid 358 through 362 Processing helix chain 'E' and resid 394 through 400 Processing helix chain 'E' and resid 404 through 417 removed outlier: 4.110A pdb=" N ASN E 408 " --> pdb=" O PRO E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 442 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 536 through 544 Processing helix chain 'E' and resid 555 through 566 Processing helix chain 'E' and resid 578 through 582 Processing helix chain 'E' and resid 590 through 594 Processing helix chain 'E' and resid 596 through 618 removed outlier: 3.706A pdb=" N THR E 600 " --> pdb=" O GLU E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 755 Processing helix chain 'E' and resid 762 through 797 Processing helix chain 'E' and resid 806 through 828 Processing helix chain 'E' and resid 829 through 833 removed outlier: 3.838A pdb=" N ARG E 833 " --> pdb=" O GLU E 830 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 290 through 301 removed outlier: 7.208A pdb=" N THR D 276 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR D 269 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA D 261 " --> pdb=" O HIS D 284 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N HIS D 264 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL D 356 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP D 244 " --> pdb=" O PRO D 354 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL D 355 " --> pdb=" O ARG D 385 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG D 385 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG D 357 " --> pdb=" O MET D 383 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET D 383 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE D 359 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU D 381 " --> pdb=" O PHE D 359 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 290 through 301 removed outlier: 7.208A pdb=" N THR D 276 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR D 269 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA D 261 " --> pdb=" O HIS D 284 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N HIS D 264 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL D 356 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP D 244 " --> pdb=" O PRO D 354 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL D 355 " --> pdb=" O ARG D 385 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ARG D 385 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG D 357 " --> pdb=" O MET D 383 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET D 383 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE D 359 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU D 381 " --> pdb=" O PHE D 359 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 222 through 224 removed outlier: 6.084A pdb=" N VAL D 222 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA E 455 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N TYR E 262 " --> pdb=" O ARG E 453 " (cutoff:3.500A) removed outlier: 11.258A pdb=" N ARG E 453 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL E 446 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARG E 476 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG E 448 " --> pdb=" O TYR E 474 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TYR E 474 " --> pdb=" O ARG E 448 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR E 450 " --> pdb=" O ILE E 472 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE E 472 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 383 through 390 removed outlier: 4.207A pdb=" N ILE E 365 " --> pdb=" O MET E 390 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU E 351 " --> pdb=" O PHE E 330 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE E 325 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR E 450 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR E 327 " --> pdb=" O ARG E 448 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG E 448 " --> pdb=" O THR E 327 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR E 329 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL E 446 " --> pdb=" O ARG E 476 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ARG E 476 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG E 448 " --> pdb=" O TYR E 474 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TYR E 474 " --> pdb=" O ARG E 448 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR E 450 " --> pdb=" O ILE E 472 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE E 472 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 474 through 475 Processing sheet with id=AA6, first strand: chain 'A' and resid 41 through 42 901 hydrogen bonds defined for protein. 2628 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2082 1.31 - 1.44: 3642 1.44 - 1.56: 7624 1.56 - 1.69: 25 1.69 - 1.82: 59 Bond restraints: 13432 Sorted by residual: bond pdb=" C21 PC1 E 901 " pdb=" O21 PC1 E 901 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C31 PC1 E 901 " pdb=" O31 PC1 E 901 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C31 PC1 D1003 " pdb=" O31 PC1 D1003 " ideal model delta sigma weight residual 1.330 1.397 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C21 PC1 D1003 " pdb=" O21 PC1 D1003 " ideal model delta sigma weight residual 1.331 1.396 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" O3 PO4 D1005 " pdb=" P PO4 D1005 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.94e+00 ... (remaining 13427 not shown) Histogram of bond angle deviations from ideal: 97.65 - 104.92: 214 104.92 - 112.18: 6853 112.18 - 119.45: 4326 119.45 - 126.72: 6610 126.72 - 133.98: 180 Bond angle restraints: 18183 Sorted by residual: angle pdb=" CA PRO E 502 " pdb=" N PRO E 502 " pdb=" CD PRO E 502 " ideal model delta sigma weight residual 112.00 98.48 13.52 1.40e+00 5.10e-01 9.33e+01 angle pdb=" CA PRO E 168 " pdb=" N PRO E 168 " pdb=" CD PRO E 168 " ideal model delta sigma weight residual 112.00 100.68 11.32 1.40e+00 5.10e-01 6.54e+01 angle pdb=" O12 PC1 E 901 " pdb=" P PC1 E 901 " pdb=" O14 PC1 E 901 " ideal model delta sigma weight residual 123.67 109.24 14.43 3.00e+00 1.11e-01 2.31e+01 angle pdb=" O12 PC1 D1003 " pdb=" P PC1 D1003 " pdb=" O14 PC1 D1003 " ideal model delta sigma weight residual 123.67 109.48 14.19 3.00e+00 1.11e-01 2.24e+01 angle pdb=" CA LEU E 57 " pdb=" CB LEU E 57 " pdb=" CG LEU E 57 " ideal model delta sigma weight residual 116.30 130.72 -14.42 3.50e+00 8.16e-02 1.70e+01 ... (remaining 18178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 7795 35.66 - 71.32: 312 71.32 - 106.98: 18 106.98 - 142.63: 18 142.63 - 178.29: 3 Dihedral angle restraints: 8146 sinusoidal: 3520 harmonic: 4626 Sorted by residual: dihedral pdb=" C4 IHP D1001 " pdb=" C2 IHP D1001 " pdb=" C3 IHP D1001 " pdb=" O12 IHP D1001 " ideal model delta sinusoidal sigma weight residual 60.90 -117.39 178.29 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O12 IHP D1001 " pdb=" C2 IHP D1001 " pdb=" C3 IHP D1001 " pdb=" O13 IHP D1001 " ideal model delta sinusoidal sigma weight residual 64.08 -121.46 -174.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C6 IHP D1004 " pdb=" C1 IHP D1004 " pdb=" C2 IHP D1004 " pdb=" O12 IHP D1004 " ideal model delta sinusoidal sigma weight residual 61.05 -153.70 -145.25 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 8143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.044: 1992 1.044 - 2.088: 0 2.088 - 3.132: 0 3.132 - 4.176: 0 4.176 - 5.221: 9 Chirality restraints: 2001 Sorted by residual: chirality pdb=" C4 IHP D1002 " pdb=" C3 IHP D1002 " pdb=" C5 IHP D1002 " pdb=" O14 IHP D1002 " both_signs ideal model delta sigma weight residual False 2.48 -2.74 5.22 2.00e-01 2.50e+01 6.81e+02 chirality pdb=" C4 IHP D1004 " pdb=" C3 IHP D1004 " pdb=" C5 IHP D1004 " pdb=" O14 IHP D1004 " both_signs ideal model delta sigma weight residual False 2.48 -2.66 5.14 2.00e-01 2.50e+01 6.61e+02 chirality pdb=" C1 IHP D1002 " pdb=" C2 IHP D1002 " pdb=" C6 IHP D1002 " pdb=" O11 IHP D1002 " both_signs ideal model delta sigma weight residual False 2.32 -2.74 5.06 2.00e-01 2.50e+01 6.39e+02 ... (remaining 1998 not shown) Planarity restraints: 2267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 167 " -0.095 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PRO E 168 " 0.233 5.00e-02 4.00e+02 pdb=" CA PRO E 168 " -0.067 5.00e-02 4.00e+02 pdb=" CD PRO E 168 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 501 " 0.084 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO E 502 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO E 502 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO E 502 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 56 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO B 57 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 57 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 57 " 0.033 5.00e-02 4.00e+02 ... (remaining 2264 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1167 2.74 - 3.28: 12900 3.28 - 3.82: 22513 3.82 - 4.36: 25668 4.36 - 4.90: 45301 Nonbonded interactions: 107549 Sorted by model distance: nonbonded pdb=" OH TYR E 409 " pdb=" O45 IHP D1004 " model vdw 2.203 2.440 nonbonded pdb=" OE2 GLU E 90 " pdb=" OG1 THR E 94 " model vdw 2.245 2.440 nonbonded pdb=" O PRO D 95 " pdb=" OG1 THR D 96 " model vdw 2.253 2.440 nonbonded pdb=" O GLY D 644 " pdb=" OG1 THR D 648 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR D 23 " pdb=" O32 IHP D1001 " model vdw 2.288 2.440 ... (remaining 107544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 55 through 156) selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 37.350 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:10.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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 : 0.004 0.139 13432 Z= 0.283 Angle : 0.812 14.426 18183 Z= 0.373 Chirality : 0.332 5.221 2001 Planarity : 0.006 0.135 2267 Dihedral : 18.798 178.292 5150 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.41 % Allowed : 19.31 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % 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: 1.69 (0.22), residues: 1554 helix: 2.06 (0.17), residues: 920 sheet: 0.41 (0.38), residues: 180 loop : -0.51 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 268 HIS 0.002 0.001 HIS E 160 PHE 0.029 0.002 PHE E 183 TYR 0.026 0.001 TYR E 198 ARG 0.012 0.000 ARG D 443 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 9 SER cc_start: 0.7566 (m) cc_final: 0.7326 (t) REVERT: D 383 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7695 (mtt) REVERT: D 443 ARG cc_start: 0.7976 (ttm-80) cc_final: 0.7705 (mtm180) REVERT: E 112 GLU cc_start: 0.7764 (pp20) cc_final: 0.7509 (pp20) REVERT: E 189 TYR cc_start: 0.7870 (m-80) cc_final: 0.7569 (m-80) REVERT: E 533 MET cc_start: 0.2802 (tpp) cc_final: 0.2522 (tpp) REVERT: E 573 ASN cc_start: 0.8132 (p0) cc_final: 0.7905 (p0) outliers start: 20 outliers final: 15 residues processed: 159 average time/residue: 1.0151 time to fit residues: 180.6261 Evaluate side-chains 145 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain E residue 825 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 0.1980 chunk 141 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN D 160 ASN D 198 GLN D 264 HIS D 335 ASN D 427 ASN D 605 GLN E 101 ASN ** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 ASN E 462 GLN E 527 ASN E 602 GLN ** E 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13432 Z= 0.186 Angle : 0.600 10.819 18183 Z= 0.284 Chirality : 0.042 0.406 2001 Planarity : 0.004 0.047 2267 Dihedral : 12.439 109.041 1979 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.17 % Allowed : 16.28 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.22), residues: 1554 helix: 2.41 (0.17), residues: 929 sheet: 0.44 (0.38), residues: 178 loop : -0.35 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 268 HIS 0.003 0.001 HIS E 256 PHE 0.020 0.001 PHE E 145 TYR 0.033 0.001 TYR E 198 ARG 0.005 0.000 ARG E 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 1.659 Fit side-chains revert: symmetry clash REVERT: D 51 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6739 (mt-10) REVERT: D 77 GLU cc_start: 0.6980 (tm-30) cc_final: 0.6752 (pp20) REVERT: D 383 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7522 (mtt) REVERT: D 440 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6787 (tm-30) REVERT: A 85 LEU cc_start: 0.8166 (tp) cc_final: 0.7928 (tp) REVERT: C 122 ARG cc_start: 0.5978 (mpt180) cc_final: 0.5734 (mmp-170) REVERT: E 53 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7863 (ptt90) REVERT: E 112 GLU cc_start: 0.7781 (pp20) cc_final: 0.7505 (pp20) REVERT: E 189 TYR cc_start: 0.7820 (m-80) cc_final: 0.7521 (m-80) REVERT: E 268 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5750 (tp30) REVERT: E 573 ASN cc_start: 0.8087 (p0) cc_final: 0.7875 (p0) outliers start: 45 outliers final: 16 residues processed: 175 average time/residue: 1.1073 time to fit residues: 214.9650 Evaluate side-chains 151 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 383 MET Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 693 ASP Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 807 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.0570 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 141 optimal weight: 0.8980 chunk 153 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 chunk 48 optimal weight: 0.2980 chunk 113 optimal weight: 20.0000 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN D 160 ASN D 335 ASN E 535 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13432 Z= 0.170 Angle : 0.525 8.623 18183 Z= 0.261 Chirality : 0.040 0.289 2001 Planarity : 0.004 0.057 2267 Dihedral : 11.717 105.020 1957 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.89 % Allowed : 16.63 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.22), residues: 1554 helix: 2.51 (0.16), residues: 931 sheet: 0.50 (0.38), residues: 177 loop : -0.50 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 268 HIS 0.002 0.001 HIS E 256 PHE 0.019 0.001 PHE B 140 TYR 0.023 0.001 TYR E 198 ARG 0.011 0.000 ARG E 738 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 440 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: D 712 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6803 (mp) REVERT: A 85 LEU cc_start: 0.8161 (tp) cc_final: 0.7884 (tp) REVERT: B 140 PHE cc_start: 0.7667 (t80) cc_final: 0.6943 (t80) REVERT: C 101 PHE cc_start: 0.7351 (t80) cc_final: 0.7129 (t80) REVERT: E 95 PHE cc_start: 0.7959 (t80) cc_final: 0.7721 (t80) REVERT: E 112 GLU cc_start: 0.7491 (pp20) cc_final: 0.7142 (pp20) REVERT: E 189 TYR cc_start: 0.7751 (m-80) cc_final: 0.7453 (m-80) REVERT: E 268 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5751 (tp30) REVERT: E 503 ASN cc_start: 0.8067 (m110) cc_final: 0.7427 (p0) REVERT: E 522 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: E 533 MET cc_start: 0.2952 (tpp) cc_final: 0.2670 (tpp) outliers start: 41 outliers final: 18 residues processed: 173 average time/residue: 1.0269 time to fit residues: 197.8800 Evaluate side-chains 157 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 693 ASP Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain E residue 807 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 160 ASN D 335 ASN A 149 ASN E 535 ASN E 844 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13432 Z= 0.251 Angle : 0.556 8.775 18183 Z= 0.276 Chirality : 0.041 0.335 2001 Planarity : 0.005 0.099 2267 Dihedral : 11.508 103.665 1954 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.66 % Allowed : 16.07 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.22), residues: 1554 helix: 2.39 (0.16), residues: 934 sheet: 0.55 (0.39), residues: 177 loop : -0.50 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 268 HIS 0.003 0.001 HIS E 242 PHE 0.018 0.002 PHE E 95 TYR 0.025 0.001 TYR D 679 ARG 0.012 0.000 ARG E 738 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 139 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 26 LEU cc_start: 0.7971 (mt) cc_final: 0.7750 (mp) REVERT: D 712 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6947 (mp) REVERT: A 85 LEU cc_start: 0.8226 (tp) cc_final: 0.7944 (tp) REVERT: E 53 ARG cc_start: 0.8316 (ptm-80) cc_final: 0.8109 (ptt90) REVERT: E 112 GLU cc_start: 0.7553 (pp20) cc_final: 0.7171 (pp20) REVERT: E 189 TYR cc_start: 0.7815 (m-80) cc_final: 0.7446 (m-80) REVERT: E 268 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5762 (tp30) REVERT: E 503 ASN cc_start: 0.8166 (m110) cc_final: 0.7462 (p0) REVERT: E 598 LYS cc_start: 0.4419 (OUTLIER) cc_final: 0.4014 (ptmt) outliers start: 52 outliers final: 25 residues processed: 174 average time/residue: 1.0403 time to fit residues: 201.7041 Evaluate side-chains 157 residues out of total 1419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain D residue 613 THR Chi-restraints excluded: chain D residue 693 ASP Chi-restraints excluded: chain D residue 697 LYS Chi-restraints excluded: chain D residue 712 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain E residue 47 SER Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 450 THR Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain E residue 556 LEU Chi-restraints excluded: chain E residue 598 LYS Chi-restraints excluded: chain E residue 753 ILE Chi-restraints excluded: chain E residue 807 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.6254 > 50: distance: 80 - 98: 9.617 distance: 86 - 106: 20.794 distance: 91 - 114: 23.106 distance: 94 - 98: 10.639 distance: 98 - 99: 6.993 distance: 99 - 100: 5.275 distance: 99 - 102: 8.444 distance: 100 - 101: 24.391 distance: 100 - 106: 10.631 distance: 102 - 103: 12.873 distance: 102 - 104: 16.755 distance: 106 - 107: 7.778 distance: 107 - 108: 20.471 distance: 107 - 110: 7.070 distance: 108 - 109: 11.046 distance: 108 - 114: 19.368 distance: 110 - 111: 11.506 distance: 111 - 112: 11.513 distance: 111 - 113: 7.660 distance: 114 - 115: 23.164 distance: 115 - 116: 5.293 distance: 115 - 118: 10.226 distance: 116 - 117: 11.344 distance: 116 - 125: 23.259 distance: 118 - 119: 24.234 distance: 119 - 120: 16.775 distance: 120 - 121: 15.423 distance: 121 - 122: 7.497 distance: 122 - 123: 8.318 distance: 122 - 124: 9.691 distance: 125 - 126: 9.971 distance: 126 - 129: 23.399 distance: 127 - 128: 20.810 distance: 127 - 135: 21.170 distance: 129 - 130: 17.199 distance: 130 - 131: 40.185 distance: 130 - 132: 18.378 distance: 131 - 133: 8.525 distance: 132 - 134: 22.827 distance: 133 - 134: 8.378 distance: 135 - 136: 25.218 distance: 136 - 137: 12.060 distance: 136 - 139: 34.742 distance: 137 - 138: 42.003 distance: 137 - 143: 3.542 distance: 139 - 140: 46.082 distance: 140 - 141: 18.436 distance: 140 - 142: 44.721 distance: 143 - 144: 24.750 distance: 143 - 149: 12.806 distance: 144 - 145: 22.006 distance: 144 - 147: 16.674 distance: 145 - 146: 31.051 distance: 145 - 150: 16.767 distance: 147 - 148: 18.606 distance: 148 - 149: 19.889 distance: 150 - 151: 6.212 distance: 151 - 152: 12.414 distance: 151 - 154: 17.847 distance: 152 - 153: 22.441 distance: 152 - 155: 12.920 distance: 155 - 156: 6.522 distance: 155 - 204: 4.958 distance: 156 - 157: 14.811 distance: 156 - 159: 10.597 distance: 157 - 158: 19.152 distance: 157 - 163: 21.662 distance: 159 - 160: 13.691 distance: 160 - 161: 4.468 distance: 160 - 162: 8.106 distance: 163 - 164: 8.313 distance: 164 - 165: 12.215 distance: 164 - 167: 10.784 distance: 165 - 166: 11.920 distance: 165 - 170: 29.212 distance: 167 - 168: 16.767 distance: 167 - 169: 31.060 distance: 170 - 171: 12.133 distance: 171 - 172: 14.767 distance: 171 - 174: 24.135 distance: 172 - 173: 18.724 distance: 172 - 182: 15.980 distance: 174 - 175: 14.131 distance: 175 - 176: 13.257 distance: 175 - 177: 9.342 distance: 176 - 178: 10.274 distance: 177 - 179: 8.934 distance: 178 - 180: 9.737 distance: 179 - 180: 10.898 distance: 180 - 181: 14.116