Starting phenix.real_space_refine on Fri Jan 19 01:40:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pma_13526/01_2024/7pma_13526_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pma_13526/01_2024/7pma_13526.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/7pma_13526/01_2024/7pma_13526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pma_13526/01_2024/7pma_13526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pma_13526/01_2024/7pma_13526_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pma_13526/01_2024/7pma_13526_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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 62 5.16 5 C 6412 2.51 5 N 1710 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 19": "OE1" <-> "OE2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 362": "OD1" <-> "OD2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ARG 710": "NH1" <-> "NH2" Residue "A TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 763": "NH1" <-> "NH2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 266": "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: 10066 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5987 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 27, 'TRANS': 704} Chain breaks: 6 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.76, per 1000 atoms: 0.57 Number of scatterers: 10066 At special positions: 0 Unit cell: (102.82, 142.04, 149.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 4 15.00 Mg 2 11.99 O 1876 8.00 N 1710 7.00 C 6412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.34 Conformation dependent library (CDL) restraints added in 1.8 seconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2352 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 12 sheets defined 49.2% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.054A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.523A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 139 through 152 Processing helix chain 'A' and resid 169 through 183 removed outlier: 3.693A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.740A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 260 through 267 Processing helix chain 'A' and resid 274 through 277 Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.624A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLY A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 291' Processing helix chain 'A' and resid 301 through 315 removed outlier: 4.367A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 336 removed outlier: 3.887A pdb=" N GLY A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 393 through 423 removed outlier: 3.699A pdb=" N LYS A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 423 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 478 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.561A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 568 removed outlier: 5.370A pdb=" N LEU A 565 " --> pdb=" O GLU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.839A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 633 No H-bonds generated for 'chain 'A' and resid 630 through 633' Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 676 through 684 Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 704 through 713 removed outlier: 4.053A pdb=" N SER A 709 " --> pdb=" O GLN A 705 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 735 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 755 through 791 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.630A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.854A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.827A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.102A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.960A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 262 removed outlier: 4.583A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.830A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 removed outlier: 4.472A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.791A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 348 removed outlier: 4.439A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 354 removed outlier: 3.989A pdb=" N GLN C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 350 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.670A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.532A pdb=" N VAL B 65 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 12 through 15 removed outlier: 7.321A pdb=" N GLN A 39 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.534A pdb=" N SER A 162 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 377 through 381 Processing sheet with id= E, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= F, first strand: chain 'A' and resid 700 through 703 Processing sheet with id= G, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.640A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 8 through 12 Processing sheet with id= I, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= J, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.636A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 435 hydrogen bonds defined for protein. 1197 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: 3.01 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1671 1.32 - 1.44: 2729 1.44 - 1.56: 5775 1.56 - 1.69: 6 1.69 - 1.81: 100 Bond restraints: 10281 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.201 0.062 2.00e-02 2.50e+03 9.59e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.463 0.062 2.10e-02 2.27e+03 8.64e+00 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.40e-02 5.10e+03 8.47e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.47e+00 ... (remaining 10276 not shown) Histogram of bond angle deviations from ideal: 97.06 - 104.86: 211 104.86 - 112.65: 5241 112.65 - 120.44: 4564 120.44 - 128.24: 3789 128.24 - 136.03: 85 Bond angle restraints: 13890 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 109.82 11.88 1.80e+00 3.09e-01 4.36e+01 angle pdb=" C LYS A 668 " pdb=" N PHE A 669 " pdb=" CA PHE A 669 " ideal model delta sigma weight residual 122.48 130.29 -7.81 1.77e+00 3.19e-01 1.95e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.79 -4.79 1.10e+00 8.26e-01 1.90e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 102.08 8.02 1.90e+00 2.77e-01 1.78e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.28 4.12 1.00e+00 1.00e+00 1.70e+01 ... (remaining 13885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.82: 6020 31.82 - 63.65: 128 63.65 - 95.47: 39 95.47 - 127.29: 3 127.29 - 159.12: 2 Dihedral angle restraints: 6192 sinusoidal: 2545 harmonic: 3647 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 99.12 -159.12 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 75.39 -135.39 1 2.00e+01 2.50e-03 4.11e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 175.57 124.43 1 2.00e+01 2.50e-03 3.76e+01 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1068 0.044 - 0.089: 300 0.089 - 0.133: 119 0.133 - 0.177: 21 0.177 - 0.222: 9 Chirality restraints: 1517 Sorted by residual: chirality pdb=" CA TYR A 10 " pdb=" N TYR A 10 " pdb=" C TYR A 10 " pdb=" CB TYR A 10 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA MET A 478 " pdb=" N MET A 478 " pdb=" C MET A 478 " pdb=" CB MET A 478 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CG LEU B 113 " pdb=" CB LEU B 113 " pdb=" CD1 LEU B 113 " pdb=" CD2 LEU B 113 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1514 not shown) Planarity restraints: 1771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 248 " -0.111 9.50e-02 1.11e+02 6.47e-02 2.29e+01 pdb=" NE ARG A 248 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 248 " -0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG A 248 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG A 248 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 89 " -0.022 2.00e-02 2.50e+03 4.41e-02 1.94e+01 pdb=" C THR C 89 " 0.076 2.00e-02 2.50e+03 pdb=" O THR C 89 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE C 90 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 231 " 0.233 9.50e-02 1.11e+02 1.08e-01 1.45e+01 pdb=" NE ARG A 231 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 231 " -0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG A 231 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 231 " 0.025 2.00e-02 2.50e+03 ... (remaining 1768 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 2 2.03 - 2.75: 1039 2.75 - 3.47: 14905 3.47 - 4.18: 23480 4.18 - 4.90: 41910 Nonbonded interactions: 81336 Sorted by model distance: nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.317 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb="MG MG A1901 " pdb=" O1B ADP A1902 " model vdw 2.060 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.073 2.170 nonbonded pdb="MG MG A1901 " pdb=" O3B ADP A1902 " model vdw 2.155 2.170 ... (remaining 81331 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 7.200 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.160 Find NCS groups from input model: 0.250 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: 0.010 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: 43.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 0.122 10281 Z= 0.265 Angle : 0.884 11.880 13890 Z= 0.515 Chirality : 0.051 0.222 1517 Planarity : 0.008 0.108 1771 Dihedral : 15.926 159.118 3840 Min Nonbonded Distance : 1.317 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % Cbeta Deviations : 0.08 % 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: -1.07 (0.21), residues: 1218 helix: -1.28 (0.17), residues: 572 sheet: 0.60 (0.37), residues: 165 loop : -0.16 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A 484 HIS 0.006 0.001 HIS B 132 PHE 0.029 0.002 PHE A 673 TYR 0.035 0.006 TYR A 113 ARG 0.080 0.012 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ILE cc_start: 0.8764 (pt) cc_final: 0.8528 (pt) outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.2404 time to fit residues: 52.1416 Evaluate side-chains 89 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 264 GLN A 354 HIS A 373 HIS A 395 HIS A 410 ASN ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 533 ASN ** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10281 Z= 0.207 Angle : 0.678 11.080 13890 Z= 0.345 Chirality : 0.044 0.222 1517 Planarity : 0.004 0.042 1771 Dihedral : 10.014 164.573 1393 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 0.84 % Allowed : 6.07 % Favored : 93.09 % 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: 1.03 (0.23), residues: 1218 helix: 0.88 (0.20), residues: 590 sheet: 0.90 (0.38), residues: 166 loop : 0.58 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 79 HIS 0.006 0.001 HIS C 275 PHE 0.029 0.002 PHE A 360 TYR 0.017 0.001 TYR A 477 ARG 0.005 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.7658 (tp40) cc_final: 0.7207 (tp-100) REVERT: B 68 GLU cc_start: 0.8713 (mp0) cc_final: 0.8458 (mp0) REVERT: A 135 MET cc_start: 0.8104 (mmm) cc_final: 0.7807 (tpp) REVERT: A 437 ASP cc_start: 0.7388 (p0) cc_final: 0.7124 (p0) outliers start: 9 outliers final: 5 residues processed: 107 average time/residue: 0.2353 time to fit residues: 36.0757 Evaluate side-chains 86 residues out of total 1082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 285 CYS 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: 66.447 > 50: distance: 39 - 140: 25.976 distance: 42 - 137: 31.863 distance: 50 - 125: 13.658 distance: 53 - 122: 24.321 distance: 97 - 102: 28.047 distance: 102 - 103: 34.087 distance: 103 - 104: 55.362 distance: 104 - 105: 34.805 distance: 104 - 106: 40.063 distance: 106 - 107: 33.436 distance: 107 - 108: 38.876 distance: 107 - 110: 37.166 distance: 108 - 109: 35.098 distance: 108 - 114: 28.695 distance: 110 - 111: 19.765 distance: 110 - 112: 24.223 distance: 111 - 113: 26.865 distance: 114 - 115: 17.346 distance: 115 - 116: 39.905 distance: 115 - 118: 31.219 distance: 116 - 117: 15.300 distance: 116 - 122: 41.577 distance: 118 - 119: 9.193 distance: 119 - 120: 19.436 distance: 119 - 121: 11.716 distance: 122 - 123: 29.198 distance: 123 - 124: 15.647 distance: 123 - 126: 39.870 distance: 124 - 125: 37.049 distance: 124 - 129: 42.909 distance: 126 - 127: 28.517 distance: 126 - 128: 27.525 distance: 129 - 130: 8.782 distance: 130 - 131: 10.984 distance: 130 - 133: 38.695 distance: 131 - 132: 17.318 distance: 131 - 137: 48.041 distance: 133 - 134: 30.232 distance: 134 - 135: 27.420 distance: 134 - 136: 21.853 distance: 137 - 138: 44.782 distance: 138 - 139: 44.392 distance: 138 - 141: 23.718 distance: 139 - 140: 58.079 distance: 139 - 146: 39.478 distance: 141 - 142: 21.974 distance: 142 - 143: 19.385 distance: 143 - 144: 11.619 distance: 144 - 145: 9.052 distance: 146 - 147: 18.450 distance: 147 - 148: 52.048 distance: 147 - 150: 48.920 distance: 148 - 149: 41.695 distance: 148 - 158: 43.425 distance: 150 - 151: 40.949 distance: 151 - 152: 18.064 distance: 151 - 153: 9.488 distance: 152 - 154: 21.416 distance: 153 - 155: 11.384 distance: 154 - 156: 19.900 distance: 155 - 156: 20.351 distance: 156 - 157: 6.153 distance: 158 - 159: 48.887 distance: 158 - 164: 32.237 distance: 159 - 160: 12.395 distance: 159 - 162: 65.703 distance: 160 - 161: 24.937 distance: 160 - 165: 35.592 distance: 162 - 163: 45.772 distance: 163 - 164: 28.241 distance: 165 - 166: 42.141 distance: 166 - 167: 49.192 distance: 166 - 169: 48.462 distance: 167 - 168: 31.000 distance: 167 - 173: 51.521 distance: 169 - 170: 37.419 distance: 169 - 171: 9.222 distance: 170 - 172: 23.998 distance: 173 - 174: 22.946 distance: 174 - 175: 11.032 distance: 174 - 177: 15.277 distance: 175 - 176: 21.658 distance: 175 - 182: 12.624 distance: 177 - 178: 12.200 distance: 178 - 179: 3.317 distance: 179 - 180: 3.600 distance: 179 - 181: 5.793