Starting phenix.real_space_refine on Fri Jan 19 00:40:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5n_12041/01_2024/7b5n_12041_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5n_12041/01_2024/7b5n_12041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5n_12041/01_2024/7b5n_12041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5n_12041/01_2024/7b5n_12041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5n_12041/01_2024/7b5n_12041_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5n_12041/01_2024/7b5n_12041_updated.pdb" } resolution = 3.6 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= 0.000 sd= 0.002 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 Zn 9 6.06 5 S 77 5.16 5 C 6321 2.51 5 N 1725 2.21 5 O 1833 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 420": "OE1" <-> "OE2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C ASP 534": "OD1" <-> "OD2" Residue "C GLU 589": "OE1" <-> "OE2" Residue "C GLU 660": "OE1" <-> "OE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 237": "OD1" <-> "OD2" Residue "H TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 271": "NH1" <-> "NH2" Residue "H ASP 280": "OD1" <-> "OD2" Residue "H TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 370": "OE1" <-> "OE2" Residue "H GLU 443": "OE1" <-> "OE2" Residue "H PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 530": "NH1" <-> "NH2" Residue "U GLU 16": "OE1" <-> "OE2" Residue "U GLU 24": "OE1" <-> "OE2" Residue "U ASP 32": "OD1" <-> "OD2" Residue "U ASP 39": "OD1" <-> "OD2" Residue "U ARG 42": "NH1" <-> "NH2" Residue "U ARG 72": "NH1" <-> "NH2" Residue "U ARG 74": "NH1" <-> "NH2" Residue "N ASP 21": "OD1" <-> "OD2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R GLU 102": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9965 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3398 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3472 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 410} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "U" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "R" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 677 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1209 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 137} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' ZN': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "U" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'SY8': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5255 SG CYS H 344 88.596 51.367 35.674 1.00 63.40 S ATOM 5277 SG CYS H 347 86.278 51.508 38.931 1.00 67.85 S ATOM 5388 SG CYS H 362 88.652 48.719 38.315 1.00 73.36 S ATOM 5427 SG CYS H 367 85.690 48.967 36.300 1.00 65.71 S ATOM 5467 SG CYS H 372 98.854 50.897 28.180 1.00 80.71 S ATOM 5494 SG CYS H 375 96.661 52.921 25.973 1.00 84.91 S ATOM 5588 SG CYS H 389 100.357 53.840 25.918 1.00121.79 S ATOM 4710 SG CYS H 276 74.024 61.875 53.700 1.00 35.62 S ATOM 4743 SG CYS H 281 71.906 59.754 55.671 1.00 42.39 S ATOM 4874 SG CYS H 297 70.375 62.156 53.287 1.00 49.44 S ATOM 4889 SG CYS H 299 72.147 63.354 56.656 1.00 55.96 S ATOM 4930 SG CYS H 304 74.535 68.765 42.090 1.00 29.12 S ATOM 4955 SG CYS H 307 78.447 68.267 42.721 1.00 31.97 S ATOM 5037 SG CYS H 317 77.181 69.509 39.463 1.00 28.90 S ATOM 3984 SG CYS H 186 86.173 17.376 47.279 1.00 86.68 S ATOM 4007 SG CYS H 189 87.143 16.632 50.772 1.00 91.82 S ATOM 4165 SG CYS H 208 83.833 17.858 50.099 1.00 77.45 S ATOM 4188 SG CYS H 211 86.634 20.319 49.968 1.00 66.51 S ATOM 4125 SG CYS H 203 78.738 23.933 36.909 1.00 86.78 S ATOM 4346 SG CYS H 231 81.354 24.858 39.376 1.00 37.03 S ATOM 4378 SG CYS H 236 81.750 25.783 35.500 1.00 50.91 S ATOM 8251 SG CYS R 42 68.670 100.376 33.343 1.00 27.14 S ATOM 8270 SG CYS R 45 68.786 99.018 37.078 1.00 22.21 S ATOM 8518 SG CYS R 83 70.525 102.157 36.148 1.00 23.15 S ATOM 8447 SG CYS R 75 72.299 101.999 20.644 1.00 23.78 S ATOM 8614 SG CYS R 94 74.157 100.704 23.838 1.00 26.05 S ATOM 8337 SG CYS R 53 68.751 104.522 40.231 1.00 26.92 S ATOM 8360 SG CYS R 56 67.762 107.652 42.111 1.00 34.82 S ATOM 8397 SG CYS R 68 66.092 106.653 38.683 1.00 28.19 S Time building chain proxies: 5.91, per 1000 atoms: 0.59 Number of scatterers: 9965 At special positions: 0 Unit cell: (135.16, 135.16, 95.92, 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) Zn 9 29.99 S 77 16.00 O 1833 8.00 N 1725 7.00 C 6321 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 additional links: simple=1, symmetry=0 Simple link: pdb=" C GLY U 75 " - pdb=" N SY8 U 101 " Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.59 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 601 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 347 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 344 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 367 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 362 " pdb=" ZN H 602 " pdb="ZN ZN H 602 " - pdb=" NE2 HIS H 382 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 372 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 389 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 375 " pdb=" ZN H 603 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 297 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 276 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 299 " pdb="ZN ZN H 603 " - pdb=" SG CYS H 281 " pdb=" ZN H 604 " pdb="ZN ZN H 604 " - pdb=" NE2 HIS H 312 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 304 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 307 " pdb="ZN ZN H 604 " - pdb=" SG CYS H 317 " pdb=" ZN H 605 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 208 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 186 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 189 " pdb="ZN ZN H 605 " - pdb=" SG CYS H 211 " pdb=" ZN H 606 " pdb="ZN ZN H 606 " - pdb=" ND1 HIS H 205 " pdb="ZN ZN H 606 " - pdb=" SG CYS H 236 " pdb="ZN ZN H 606 " - pdb=" SG CYS H 203 " pdb="ZN ZN H 606 " - pdb=" SG CYS H 231 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " Number of angles added : 33 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 6 sheets defined 44.9% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'C' and resid 337 through 353 removed outlier: 3.574A pdb=" N THR C 342 " --> pdb=" O LYS C 338 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C 350 " --> pdb=" O ASN C 346 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C 351 " --> pdb=" O GLN C 347 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 363 through 383 removed outlier: 3.891A pdb=" N SER C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 404 Processing helix chain 'C' and resid 407 through 412 removed outlier: 3.506A pdb=" N ALA C 412 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 430 Processing helix chain 'C' and resid 439 through 455 Processing helix chain 'C' and resid 461 through 475 Processing helix chain 'C' and resid 482 through 496 Processing helix chain 'C' and resid 502 through 527 removed outlier: 3.965A pdb=" N ILE C 511 " --> pdb=" O MET C 507 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN C 527 " --> pdb=" O LYS C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 573 removed outlier: 3.557A pdb=" N ARG C 573 " --> pdb=" O PHE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 615 removed outlier: 3.558A pdb=" N TYR C 614 " --> pdb=" O ILE C 610 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN C 615 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 629 removed outlier: 3.544A pdb=" N SER C 628 " --> pdb=" O GLN C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 645 Processing helix chain 'C' and resid 706 through 721 Processing helix chain 'C' and resid 727 through 737 Processing helix chain 'C' and resid 746 through 758 Processing helix chain 'H' and resid 106 through 124 removed outlier: 3.910A pdb=" N MET H 113 " --> pdb=" O ILE H 109 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL H 114 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL H 123 " --> pdb=" O GLU H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 138 removed outlier: 3.551A pdb=" N PHE H 138 " --> pdb=" O LEU H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 150 Processing helix chain 'H' and resid 155 through 161 Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 209 through 222 Processing helix chain 'H' and resid 242 through 248 Processing helix chain 'H' and resid 253 through 269 Processing helix chain 'H' and resid 317 through 325 Processing helix chain 'H' and resid 333 through 340 Processing helix chain 'H' and resid 409 through 429 Processing helix chain 'H' and resid 431 through 447 Processing helix chain 'H' and resid 453 through 480 removed outlier: 3.951A pdb=" N TYR H 474 " --> pdb=" O ALA H 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 486 through 512 removed outlier: 3.552A pdb=" N ILE H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE H 491 " --> pdb=" O GLN H 487 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA H 496 " --> pdb=" O GLU H 492 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP H 497 " --> pdb=" O ASN H 493 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU H 510 " --> pdb=" O SER H 506 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG H 511 " --> pdb=" O GLY H 507 " (cutoff:3.500A) Processing helix chain 'H' and resid 518 through 549 removed outlier: 4.263A pdb=" N GLN H 523 " --> pdb=" O GLN H 519 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 33 Processing helix chain 'N' and resid 23 through 34 removed outlier: 4.358A pdb=" N LYS N 33 " --> pdb=" O ARG N 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 90 Processing helix chain 'D' and resid 2 through 17 removed outlier: 3.621A pdb=" N LYS D 9 " --> pdb=" O ARG D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 123 through 131 Processing helix chain 'D' and resid 133 through 147 removed outlier: 4.149A pdb=" N LYS D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU D 141 " --> pdb=" O ALA D 137 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 762 through 764 Processing sheet with id= B, first strand: chain 'H' and resid 294 through 296 Processing sheet with id= C, first strand: chain 'U' and resid 13 through 16 Processing sheet with id= D, first strand: chain 'N' and resid 2 through 6 Processing sheet with id= E, first strand: chain 'R' and resid 70 through 73 removed outlier: 3.722A pdb=" N HIS R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 34 through 39 removed outlier: 3.829A pdb=" N PHE D 51 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS D 67 " --> pdb=" O ASN D 56 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1188 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: 2.48 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3250 1.34 - 1.46: 2207 1.46 - 1.59: 4587 1.59 - 1.71: 0 1.71 - 1.83: 108 Bond restraints: 10152 Sorted by residual: bond pdb=" N PRO C 437 " pdb=" CA PRO C 437 " ideal model delta sigma weight residual 1.469 1.540 -0.070 1.22e-02 6.72e+03 3.32e+01 bond pdb=" C ASN C 436 " pdb=" N PRO C 437 " ideal model delta sigma weight residual 1.333 1.382 -0.049 1.17e-02 7.31e+03 1.79e+01 bond pdb=" C ASP C 532 " pdb=" N LEU C 533 " ideal model delta sigma weight residual 1.331 1.273 0.058 1.51e-02 4.39e+03 1.49e+01 bond pdb=" N GLU C 438 " pdb=" CA GLU C 438 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.30e-02 5.92e+03 6.46e+00 bond pdb=" CB TRP R 33 " pdb=" CG TRP R 33 " ideal model delta sigma weight residual 1.498 1.423 0.075 3.10e-02 1.04e+03 5.93e+00 ... (remaining 10147 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.24: 219 106.24 - 113.22: 5535 113.22 - 120.19: 3807 120.19 - 127.17: 4020 127.17 - 134.15: 110 Bond angle restraints: 13691 Sorted by residual: angle pdb=" C ASN C 436 " pdb=" N PRO C 437 " pdb=" CA PRO C 437 " ideal model delta sigma weight residual 119.90 128.47 -8.57 1.05e+00 9.07e-01 6.66e+01 angle pdb=" C GLU C 529 " pdb=" N PRO C 530 " pdb=" CA PRO C 530 " ideal model delta sigma weight residual 119.83 124.44 -4.61 1.08e+00 8.57e-01 1.83e+01 angle pdb=" CA GLY H 355 " pdb=" C GLY H 355 " pdb=" N GLY H 356 " ideal model delta sigma weight residual 114.65 117.77 -3.12 9.20e-01 1.18e+00 1.15e+01 angle pdb=" C GLN H 456 " pdb=" N PHE H 457 " pdb=" CA PHE H 457 " ideal model delta sigma weight residual 120.28 115.65 4.63 1.44e+00 4.82e-01 1.03e+01 angle pdb=" CA PRO C 437 " pdb=" N PRO C 437 " pdb=" CD PRO C 437 " ideal model delta sigma weight residual 112.00 107.68 4.32 1.40e+00 5.10e-01 9.53e+00 ... (remaining 13686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5458 17.93 - 35.85: 620 35.85 - 53.78: 100 53.78 - 71.71: 14 71.71 - 89.63: 15 Dihedral angle restraints: 6207 sinusoidal: 2573 harmonic: 3634 Sorted by residual: dihedral pdb=" CA PHE D 51 " pdb=" C PHE D 51 " pdb=" N ARG D 52 " pdb=" CA ARG D 52 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ASP R 97 " pdb=" C ASP R 97 " pdb=" N ASN R 98 " pdb=" CA ASN R 98 " ideal model delta harmonic sigma weight residual 180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA PRO C 530 " pdb=" C PRO C 530 " pdb=" N LEU C 531 " pdb=" CA LEU C 531 " ideal model delta harmonic sigma weight residual 180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 6204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 975 0.041 - 0.082: 398 0.082 - 0.123: 103 0.123 - 0.165: 23 0.165 - 0.206: 4 Chirality restraints: 1503 Sorted by residual: chirality pdb=" CB ILE C 344 " pdb=" CA ILE C 344 " pdb=" CG1 ILE C 344 " pdb=" CG2 ILE C 344 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE H 513 " pdb=" CA ILE H 513 " pdb=" CG1 ILE H 513 " pdb=" CG2 ILE H 513 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA TYR H 529 " pdb=" N TYR H 529 " pdb=" C TYR H 529 " pdb=" CB TYR H 529 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.11e-01 ... (remaining 1500 not shown) Planarity restraints: 1752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 664 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.01e+00 pdb=" N PRO C 665 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 665 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 665 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 509 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C LEU H 509 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU H 509 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU H 510 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 380 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO H 381 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 381 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 381 " -0.025 5.00e-02 4.00e+02 ... (remaining 1749 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 102 2.58 - 3.16: 8582 3.16 - 3.74: 14878 3.74 - 4.32: 19623 4.32 - 4.90: 32321 Nonbonded interactions: 75506 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.998 2.230 nonbonded pdb=" O ARG H 408 " pdb=" NH1 ARG H 408 " model vdw 2.166 2.520 nonbonded pdb=" O ASN C 406 " pdb=" OG1 THR C 409 " model vdw 2.226 2.440 nonbonded pdb=" NE2 GLN H 523 " pdb=" OD2 ASP H 527 " model vdw 2.240 2.520 nonbonded pdb=" NH2 ARG D 15 " pdb=" O ILE D 25 " model vdw 2.247 2.520 ... (remaining 75501 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=0.50 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: 3.650 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: 7.030 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 32.070 Find NCS groups from input model: 0.280 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.007 0.075 10152 Z= 0.439 Angle : 0.791 10.479 13691 Z= 0.453 Chirality : 0.048 0.206 1503 Planarity : 0.004 0.050 1751 Dihedral : 15.391 89.633 3838 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.09 % Allowed : 0.37 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -1.35 (0.23), residues: 1209 helix: 0.59 (0.21), residues: 569 sheet: -0.64 (0.59), residues: 86 loop : -2.65 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 33 HIS 0.005 0.001 HIS R 80 PHE 0.025 0.002 PHE D 143 TYR 0.019 0.002 TYR C 455 ARG 0.009 0.001 ARG C 473 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.211 Fit side-chains REVERT: C 531 LEU cc_start: 0.8154 (pt) cc_final: 0.7948 (pt) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.2292 time to fit residues: 52.0358 Evaluate side-chains 136 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 432 HIS ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN D 106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10152 Z= 0.250 Angle : 0.592 7.967 13691 Z= 0.310 Chirality : 0.043 0.156 1503 Planarity : 0.004 0.043 1751 Dihedral : 4.835 28.831 1327 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.28 % Allowed : 10.07 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.78 (0.24), residues: 1209 helix: 1.16 (0.22), residues: 573 sheet: -0.46 (0.62), residues: 79 loop : -2.46 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 452 HIS 0.008 0.001 HIS C 727 PHE 0.033 0.002 PHE H 457 TYR 0.027 0.001 TYR H 529 ARG 0.003 0.000 ARG C 473 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2418 Ramachandran restraints generated. 1209 Oldfield, 0 Emsley, 1209 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 38 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7488 (tt) outliers start: 14 outliers final: 10 residues processed: 163 average time/residue: 0.2345 time to fit residues: 53.7257 Evaluate side-chains 148 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 738 LEU Chi-restraints excluded: chain H residue 407 SER Chi-restraints excluded: chain U residue 36 ILE Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 51 PHE Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 107 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: 72.0551 > 50: distance: 69 - 73: 35.896 distance: 73 - 79: 39.810 distance: 74 - 75: 39.041 distance: 74 - 77: 69.668 distance: 75 - 76: 38.941 distance: 75 - 80: 4.315 distance: 78 - 79: 50.707 distance: 81 - 82: 39.897 distance: 81 - 84: 57.454 distance: 82 - 83: 39.286 distance: 85 - 86: 39.981 distance: 85 - 87: 39.613 distance: 88 - 89: 30.192 distance: 89 - 90: 50.265 distance: 89 - 92: 48.724 distance: 90 - 91: 40.259 distance: 93 - 94: 20.801 distance: 94 - 95: 31.226 distance: 95 - 96: 14.813 distance: 96 - 98: 28.546 distance: 99 - 100: 69.456 distance: 100 - 101: 49.241 distance: 100 - 103: 41.252 distance: 101 - 102: 41.765 distance: 101 - 104: 28.372 distance: 102 - 125: 6.149 distance: 104 - 105: 45.157 distance: 105 - 106: 60.907 distance: 105 - 108: 18.373 distance: 106 - 112: 41.209 distance: 107 - 130: 41.369 distance: 108 - 109: 39.942 distance: 109 - 110: 8.328 distance: 113 - 116: 56.660 distance: 114 - 120: 45.448 distance: 115 - 139: 54.390 distance: 117 - 118: 49.138 distance: 120 - 121: 42.326 distance: 121 - 122: 45.751 distance: 121 - 124: 13.043 distance: 122 - 123: 40.966 distance: 122 - 125: 50.194 distance: 123 - 151: 35.990 distance: 125 - 126: 4.600 distance: 126 - 127: 43.985 distance: 126 - 129: 40.224 distance: 127 - 128: 35.750 distance: 127 - 130: 23.344 distance: 128 - 157: 27.594 distance: 130 - 131: 60.706 distance: 131 - 132: 46.726 distance: 131 - 134: 18.282 distance: 132 - 133: 39.058 distance: 132 - 139: 40.611 distance: 134 - 135: 56.425 distance: 135 - 136: 9.844 distance: 136 - 137: 10.297 distance: 136 - 138: 3.884 distance: 139 - 140: 21.733 distance: 140 - 141: 43.611 distance: 140 - 143: 22.215 distance: 141 - 142: 66.187 distance: 141 - 151: 33.262 distance: 143 - 144: 40.421 distance: 144 - 145: 39.535 distance: 145 - 147: 32.845 distance: 147 - 149: 32.930 distance: 148 - 149: 39.478 distance: 149 - 150: 56.159