Starting phenix.real_space_refine on Wed Jan 17 23:22:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpo_32686/01_2024/7wpo_32686.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpo_32686/01_2024/7wpo_32686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpo_32686/01_2024/7wpo_32686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpo_32686/01_2024/7wpo_32686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpo_32686/01_2024/7wpo_32686.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpo_32686/01_2024/7wpo_32686.pdb" } resolution = 3.5 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= 0.005 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4371 2.51 5 N 1155 2.21 5 O 1263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 425": "OE1" <-> "OE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6829 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5279 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 27, 'TRANS': 652} Chain breaks: 1 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 34, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 15} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1325 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.64, per 1000 atoms: 0.68 Number of scatterers: 6829 At special positions: 0 Unit cell: (95.94, 87.74, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1263 8.00 N 1155 7.00 C 4371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 142 " distance=2.17 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.07 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 410 " distance=2.02 Simple disulfide: pdb=" SG CYS B 428 " - pdb=" SG CYS B 481 " distance=2.03 Simple disulfide: pdb=" SG CYS B 505 " - pdb=" SG CYS B 526 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG P 1 " - " NAG P 2 " BETA1-6 " NAG P 1 " - " FUC P 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 801 " - " ASN A 432 " " NAG A 802 " - " ASN A 91 " " NAG A 803 " - " ASN A 688 " " NAG A 804 " - " ASN A 546 " " NAG B 601 " - " ASN B 488 " " NAG C 1 " - " ASN A 54 " " NAG E 1 " - " ASN A 104 " " NAG G 1 " - " ASN A 280 " " NAG P 1 " - " ASN A 329 " Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.3 seconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 7 sheets defined 58.4% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 21 through 54 Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.792A pdb=" N GLU A 88 " --> pdb=" O PRO A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 removed outlier: 3.763A pdb=" N GLN A 103 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.757A pdb=" N VAL A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix removed outlier: 4.100A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 282 removed outlier: 4.431A pdb=" N ASN A 280 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.619A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.753A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 397 through 414 removed outlier: 3.847A pdb=" N HIS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 433 through 447 Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.950A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.618A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'A' and resid 635 through 656 Processing helix chain 'A' and resid 664 through 666 No H-bonds generated for 'chain 'A' and resid 664 through 666' Processing helix chain 'A' and resid 694 through 705 Processing helix chain 'B' and resid 413 through 421 removed outlier: 3.813A pdb=" N SER B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 452 through 460 removed outlier: 4.944A pdb=" N SER B 457 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 523 through 531 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 210 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.203A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA5, first strand: chain 'A' and resid 617 through 620 Processing sheet with id=AA6, first strand: chain 'B' and resid 403 through 407 removed outlier: 3.536A pdb=" N LEU B 564 " --> pdb=" O VAL B 487 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.451A pdb=" N SER B 552 " --> pdb=" O THR B 503 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N CYS B 505 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG B 550 " --> pdb=" O CYS B 505 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR B 507 " --> pdb=" O PRO B 548 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 1023 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: 1.95 Time building geometry restraints manager: 3.30 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: 1109 1.31 - 1.45: 2091 1.45 - 1.59: 3733 1.59 - 1.72: 8 1.72 - 1.86: 66 Bond restraints: 7007 Sorted by residual: bond pdb=" N PRO A 583 " pdb=" CD PRO A 583 " ideal model delta sigma weight residual 1.473 1.349 0.124 1.40e-02 5.10e+03 7.88e+01 bond pdb=" CA ASN A 658 " pdb=" C ASN A 658 " ideal model delta sigma weight residual 1.524 1.614 -0.090 1.40e-02 5.10e+03 4.16e+01 bond pdb=" CA ASN A 330 " pdb=" C ASN A 330 " ideal model delta sigma weight residual 1.523 1.604 -0.081 1.37e-02 5.33e+03 3.51e+01 bond pdb=" C ASN A 329 " pdb=" O ASN A 329 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.23e-02 6.61e+03 2.15e+01 bond pdb=" CB LEU A 456 " pdb=" CG LEU A 456 " ideal model delta sigma weight residual 1.530 1.618 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 7002 not shown) Histogram of bond angle deviations from ideal: 95.42 - 103.16: 108 103.16 - 110.90: 2455 110.90 - 118.64: 2965 118.64 - 126.38: 3893 126.38 - 134.12: 122 Bond angle restraints: 9543 Sorted by residual: angle pdb=" N LEU A 222 " pdb=" CA LEU A 222 " pdb=" C LEU A 222 " ideal model delta sigma weight residual 111.36 97.31 14.05 1.09e+00 8.42e-01 1.66e+02 angle pdb=" N ASN A 330 " pdb=" CA ASN A 330 " pdb=" C ASN A 330 " ideal model delta sigma weight residual 112.23 126.64 -14.41 1.26e+00 6.30e-01 1.31e+02 angle pdb=" N SER A 331 " pdb=" CA SER A 331 " pdb=" C SER A 331 " ideal model delta sigma weight residual 110.41 122.93 -12.52 1.23e+00 6.61e-01 1.04e+02 angle pdb=" N ALA A 701 " pdb=" CA ALA A 701 " pdb=" C ALA A 701 " ideal model delta sigma weight residual 111.07 100.55 10.52 1.07e+00 8.73e-01 9.67e+01 angle pdb=" N ARG A 255 " pdb=" CA ARG A 255 " pdb=" C ARG A 255 " ideal model delta sigma weight residual 113.88 102.89 10.99 1.23e+00 6.61e-01 7.98e+01 ... (remaining 9538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.33: 4161 21.33 - 42.65: 107 42.65 - 63.98: 14 63.98 - 85.31: 13 85.31 - 106.63: 4 Dihedral angle restraints: 4299 sinusoidal: 1742 harmonic: 2557 Sorted by residual: dihedral pdb=" CB CYS B 386 " pdb=" SG CYS B 386 " pdb=" SG CYS B 410 " pdb=" CB CYS B 410 " ideal model delta sinusoidal sigma weight residual 93.00 39.32 53.68 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" N VAL A 293 " pdb=" C VAL A 293 " pdb=" CA VAL A 293 " pdb=" CB VAL A 293 " ideal model delta harmonic sigma weight residual 123.40 108.02 15.38 0 2.50e+00 1.60e-01 3.78e+01 dihedral pdb=" C ILE A 291 " pdb=" N ILE A 291 " pdb=" CA ILE A 291 " pdb=" CB ILE A 291 " ideal model delta harmonic sigma weight residual -122.00 -109.69 -12.31 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 4296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 807 0.106 - 0.212: 208 0.212 - 0.319: 45 0.319 - 0.425: 22 0.425 - 0.531: 4 Chirality restraints: 1086 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.12e+02 chirality pdb=" C1 MAN C 5 " pdb=" O6 BMA C 3 " pdb=" C2 MAN C 5 " pdb=" O5 MAN C 5 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.52e+01 chirality pdb=" C1 FUC P 3 " pdb=" O6 NAG P 1 " pdb=" C2 FUC P 3 " pdb=" O5 FUC P 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.07e+01 ... (remaining 1083 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " 0.046 2.00e-02 2.50e+03 4.91e-02 3.01e+01 pdb=" CG ASN A 329 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 315 " -0.054 2.00e-02 2.50e+03 2.99e-02 1.79e+01 pdb=" CG TYR A 315 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 315 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 315 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR A 315 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 315 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 315 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 315 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 432 " 0.032 2.00e-02 2.50e+03 3.47e-02 1.50e+01 pdb=" CG ASN A 432 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 432 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 432 " -0.055 2.00e-02 2.50e+03 pdb=" C1 NAG A 801 " 0.042 2.00e-02 2.50e+03 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2404 2.87 - 3.38: 6468 3.38 - 3.88: 11286 3.88 - 4.39: 13258 4.39 - 4.90: 21324 Nonbonded interactions: 54740 Sorted by model distance: nonbonded pdb=" OD1 ASP A 700 " pdb=" N ALA A 701 " model vdw 2.359 2.520 nonbonded pdb=" NZ LYS A 187 " pdb=" OD2 ASP A 509 " model vdw 2.441 2.520 nonbonded pdb=" O ILE B 491 " pdb=" N ILE B 493 " model vdw 2.442 2.520 nonbonded pdb=" O ARG A 575 " pdb=" CG2 THR A 576 " model vdw 2.445 3.460 nonbonded pdb=" N ASP A 292 " pdb=" O ASP A 292 " model vdw 2.446 2.496 ... (remaining 54735 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 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 3.900 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.510 Find NCS groups from input model: 0.170 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 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 : 0.014 0.124 7007 Z= 0.902 Angle : 1.645 19.617 9543 Z= 1.119 Chirality : 0.112 0.531 1086 Planarity : 0.006 0.049 1197 Dihedral : 11.464 106.634 2631 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.56 % Favored : 97.32 % Rotamer: Outliers : 0.48 % Allowed : 1.77 % Favored : 97.75 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 859 helix: -0.21 (0.22), residues: 431 sheet: 0.95 (0.53), residues: 77 loop : 0.07 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP A 203 HIS 0.004 0.001 HIS A 401 PHE 0.033 0.004 PHE B 451 TYR 0.054 0.005 TYR A 315 ARG 0.005 0.001 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 194 time to evaluate : 0.818 Fit side-chains revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8102 (t80) cc_final: 0.7811 (t80) REVERT: A 506 VAL cc_start: 0.8447 (t) cc_final: 0.8245 (t) REVERT: A 651 ARG cc_start: 0.6204 (ttm-80) cc_final: 0.4840 (ttt180) outliers start: 3 outliers final: 1 residues processed: 196 average time/residue: 0.2096 time to fit residues: 53.2778 Evaluate side-chains 111 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN A 103 GLN A 141 GLN A 159 HIS A 221 GLN A 635 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7007 Z= 0.212 Angle : 0.611 8.399 9543 Z= 0.325 Chirality : 0.043 0.207 1086 Planarity : 0.004 0.033 1197 Dihedral : 7.951 72.099 1250 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.61 % Allowed : 10.45 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.28), residues: 859 helix: 1.35 (0.24), residues: 439 sheet: -0.10 (0.51), residues: 95 loop : 0.87 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 165 HIS 0.005 0.001 HIS A 42 PHE 0.016 0.002 PHE B 451 TYR 0.014 0.002 TYR A 385 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 127 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8179 (t80) cc_final: 0.7805 (t80) REVERT: A 243 TYR cc_start: 0.8498 (t80) cc_final: 0.8176 (t80) REVERT: A 568 TYR cc_start: 0.8499 (t80) cc_final: 0.8189 (t80) REVERT: A 651 ARG cc_start: 0.6428 (ttm-80) cc_final: 0.4889 (ttp-170) REVERT: B 532 ASN cc_start: 0.8962 (m-40) cc_final: 0.8735 (m-40) outliers start: 10 outliers final: 6 residues processed: 136 average time/residue: 0.1597 time to fit residues: 30.6555 Evaluate side-chains 105 residues out of total 773 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 419 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.0975 > 50: distance: 86 - 91: 34.287 distance: 91 - 92: 33.504 distance: 92 - 93: 48.852 distance: 93 - 94: 35.841 distance: 93 - 95: 39.950 distance: 96 - 97: 39.302 distance: 96 - 99: 39.521 distance: 97 - 101: 56.791 distance: 102 - 103: 41.449 distance: 102 - 105: 40.456 distance: 103 - 109: 39.005 distance: 106 - 108: 58.300 distance: 109 - 115: 39.701 distance: 110 - 111: 40.560 distance: 111 - 112: 39.472 distance: 111 - 116: 40.564 distance: 113 - 114: 55.862 distance: 114 - 115: 39.105 distance: 116 - 117: 39.522 distance: 117 - 118: 15.621 distance: 117 - 120: 41.020 distance: 118 - 119: 17.434 distance: 118 - 121: 29.548 distance: 121 - 122: 29.305 distance: 122 - 123: 40.988 distance: 122 - 125: 26.751 distance: 123 - 124: 40.042 distance: 123 - 131: 39.375 distance: 125 - 126: 40.970 distance: 126 - 127: 38.753 distance: 126 - 128: 40.081 distance: 127 - 129: 57.179 distance: 128 - 130: 38.745 distance: 129 - 130: 39.279 distance: 132 - 133: 41.035 distance: 132 - 135: 38.652 distance: 133 - 134: 39.935 distance: 133 - 139: 38.985 distance: 135 - 136: 54.552 distance: 136 - 137: 40.533 distance: 136 - 138: 57.240 distance: 139 - 140: 55.950 distance: 140 - 141: 38.897 distance: 140 - 143: 56.522 distance: 141 - 147: 41.106 distance: 144 - 145: 39.735 distance: 147 - 148: 56.063 distance: 148 - 149: 57.317 distance: 149 - 150: 49.262 distance: 149 - 151: 57.586 distance: 152 - 153: 39.614 distance: 152 - 155: 39.309 distance: 153 - 154: 56.347 distance: 153 - 159: 34.380 distance: 155 - 156: 41.151 distance: 156 - 157: 39.848