Starting phenix.real_space_refine on Fri Jan 19 02:25:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm8_13524/01_2024/7pm8_13524_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm8_13524/01_2024/7pm8_13524.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/7pm8_13524/01_2024/7pm8_13524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm8_13524/01_2024/7pm8_13524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm8_13524/01_2024/7pm8_13524_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm8_13524/01_2024/7pm8_13524_updated.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= 0.000 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 63 5.16 5 C 6462 2.51 5 N 1724 2.21 5 O 1894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A PHE 262": "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 PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ASP 719": "OD1" <-> "OD2" Residue "A ASP 738": "OD1" <-> "OD2" Residue "A TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 211": "OD1" <-> "OD2" 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: 10149 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: "A" Number of atoms: 6070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 6070 Classifications: {'peptide': 743} Link IDs: {'PTRANS': 27, 'TRANS': 715} Chain breaks: 5 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: "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: 5.74, per 1000 atoms: 0.57 Number of scatterers: 10149 At special positions: 0 Unit cell: (114.48, 142.04, 145.22, 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 63 16.00 P 4 15.00 Mg 2 11.99 O 1894 8.00 N 1724 7.00 C 6462 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: 3.98 Conformation dependent library (CDL) restraints added in 1.7 seconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 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: 2374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 13 sheets defined 49.2% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 139 through 152 removed outlier: 3.524A pdb=" N ALA A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 184 Processing helix chain 'A' and resid 192 through 207 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: 3.661A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 5.570A 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: 3.576A pdb=" N MET A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.644A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.601A pdb=" N ILE A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 removed outlier: 3.500A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 removed outlier: 3.723A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 480 Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.834A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 499 " --> pdb=" O CYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.602A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.648A pdb=" N ALA A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 574 through 581 Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.073A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 633 Processing helix chain 'A' and resid 636 through 651 Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.706A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 704 through 714 removed outlier: 6.259A pdb=" N VAL A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 734 removed outlier: 4.737A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYS A 734 " --> pdb=" O ASN A 730 " (cutoff:3.500A) 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 753 through 791 removed outlier: 3.906A pdb=" N VAL A 756 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 778 " --> pdb=" O GLN A 775 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP A 781 " --> pdb=" O ILE A 778 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR A 787 " --> pdb=" O ARG A 784 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 788 " --> pdb=" O LYS A 785 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 789 " --> pdb=" O LYS A 786 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 790 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.217A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.718A 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: 4.367A 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 'C' and resid 55 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 Processing helix chain 'C' and resid 113 through 125 removed outlier: 3.758A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.893A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.686A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.867A 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 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 252 through 262 removed outlier: 4.080A 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: 3.664A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 295 removed outlier: 4.605A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.648A 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: 3.593A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 4.244A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.544A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 372 Processing sheet with id= A, first strand: chain 'A' and resid 12 through 16 Processing sheet with id= B, first strand: chain 'A' and resid 101 through 103 Processing sheet with id= C, first strand: chain 'A' and resid 655 through 658 removed outlier: 3.719A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.937A 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 380 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 removed outlier: 3.791A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= H, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= I, first strand: chain 'C' and resid 8 through 12 removed outlier: 3.541A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= L, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.412A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 238 through 241 419 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 4.31 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: 1687 1.32 - 1.44: 2743 1.44 - 1.56: 5827 1.56 - 1.68: 6 1.68 - 1.81: 102 Bond restraints: 10365 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 3.72e+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 9.49e+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 8.67e+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 8.59e+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 7.69e+00 ... (remaining 10360 not shown) Histogram of bond angle deviations from ideal: 97.58 - 105.33: 225 105.33 - 113.08: 5517 113.08 - 120.83: 5076 120.83 - 128.58: 3110 128.58 - 136.33: 75 Bond angle restraints: 14003 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 121.70 109.78 11.92 1.80e+00 3.09e-01 4.38e+01 angle pdb=" C TYR A 113 " pdb=" N GLU A 114 " pdb=" CA GLU A 114 " ideal model delta sigma weight residual 121.75 129.28 -7.53 1.73e+00 3.34e-01 1.90e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.78 -4.78 1.10e+00 8.26e-01 1.89e+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 122.40 118.25 4.15 1.00e+00 1.00e+00 1.72e+01 ... (remaining 13998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.71: 6086 31.71 - 63.42: 123 63.42 - 95.13: 37 95.13 - 126.84: 1 126.84 - 158.56: 2 Dihedral angle restraints: 6249 sinusoidal: 2568 harmonic: 3681 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 98.55 -158.56 1 2.00e+01 2.50e-03 4.63e+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 73.47 -133.47 1 2.00e+01 2.50e-03 4.05e+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 300.00 179.67 120.34 1 2.00e+01 2.50e-03 3.61e+01 ... (remaining 6246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1091 0.047 - 0.094: 307 0.094 - 0.141: 109 0.141 - 0.188: 19 0.188 - 0.234: 4 Chirality restraints: 1530 Sorted by residual: chirality pdb=" CA TYR A 787 " pdb=" N TYR A 787 " pdb=" C TYR A 787 " pdb=" CB TYR A 787 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C2' ADP C 401 " pdb=" C1' ADP C 401 " pdb=" C3' ADP C 401 " pdb=" O2' ADP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ARG A 213 " pdb=" N ARG A 213 " pdb=" C ARG A 213 " pdb=" CB ARG A 213 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1527 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 95 " -0.128 9.50e-02 1.11e+02 7.43e-02 2.97e+01 pdb=" NE ARG C 95 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C 95 " -0.090 2.00e-02 2.50e+03 pdb=" NH1 ARG C 95 " 0.032 2.00e-02 2.50e+03 pdb=" NH2 ARG C 95 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " -0.370 9.50e-02 1.11e+02 1.69e-01 2.80e+01 pdb=" NE ARG A 213 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " 0.062 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 89 " -0.023 2.00e-02 2.50e+03 4.54e-02 2.06e+01 pdb=" C THR C 89 " 0.079 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 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 2 2.03 - 2.75: 1083 2.75 - 3.47: 14907 3.47 - 4.18: 23530 4.18 - 4.90: 42441 Nonbonded interactions: 81963 Sorted by model distance: nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.316 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 2.074 2.170 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.162 2.440 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.166 2.170 ... (remaining 81958 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: 0.010 Normalize map: mean=0, sd=1: 1.410 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: 6.990 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.610 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: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 10365 Z= 0.280 Angle : 0.882 11.918 14003 Z= 0.512 Chirality : 0.051 0.234 1530 Planarity : 0.009 0.169 1786 Dihedral : 15.704 158.556 3875 Min Nonbonded Distance : 1.316 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.81 % 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: -1.60 (0.21), residues: 1231 helix: -1.64 (0.17), residues: 587 sheet: 0.15 (0.39), residues: 144 loop : -0.41 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 79 HIS 0.007 0.002 HIS C 275 PHE 0.034 0.002 PHE A 673 TYR 0.033 0.006 TYR A 113 ARG 0.091 0.010 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.238 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: symmetry clash revert: symmetry clash REVERT: A 735 LEU cc_start: 0.8656 (mt) cc_final: 0.8355 (mp) REVERT: B 29 TYR cc_start: 0.8073 (m-80) cc_final: 0.7713 (m-80) outliers start: 1 outliers final: 1 residues processed: 160 average time/residue: 0.2653 time to fit residues: 57.2311 Evaluate side-chains 90 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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: 125 random chunks: chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 200 ASN A 264 GLN A 395 HIS A 463 GLN A 468 HIS A 755 GLN B 75 GLN B 147 HIS C 12 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 162 ASN C 173 HIS ** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10365 Z= 0.194 Angle : 0.648 7.456 14003 Z= 0.338 Chirality : 0.044 0.243 1530 Planarity : 0.005 0.048 1786 Dihedral : 9.821 170.903 1405 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.11 % Allowed : 6.48 % Favored : 92.41 % 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: 0.27 (0.23), residues: 1231 helix: 0.33 (0.20), residues: 610 sheet: 0.57 (0.39), residues: 145 loop : 0.09 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 340 HIS 0.015 0.001 HIS C 275 PHE 0.028 0.002 PHE B 19 TYR 0.039 0.001 TYR A 179 ARG 0.007 0.001 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.205 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: H 1 TRP cc_start: 0.6956 (m100) cc_final: 0.6706 (m100) REVERT: A 790 MET cc_start: 0.1159 (ptt) cc_final: -0.0373 (ttm) REVERT: B 36 MET cc_start: 0.7687 (mtt) cc_final: 0.7472 (mmt) REVERT: B 120 MET cc_start: 0.4786 (mtt) cc_final: 0.4574 (mmm) REVERT: C 325 MET cc_start: 0.8091 (mmt) cc_final: 0.7717 (mmt) outliers start: 12 outliers final: 6 residues processed: 112 average time/residue: 0.2338 time to fit residues: 37.0615 Evaluate side-chains 87 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain C residue 226 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 113 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10365 Z= 0.237 Angle : 0.596 8.051 14003 Z= 0.307 Chirality : 0.042 0.196 1530 Planarity : 0.004 0.048 1786 Dihedral : 9.313 170.709 1405 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.02 % Allowed : 8.33 % Favored : 90.66 % 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: 0.64 (0.23), residues: 1231 helix: 0.75 (0.21), residues: 613 sheet: 0.86 (0.41), residues: 144 loop : 0.03 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 79 HIS 0.011 0.001 HIS C 275 PHE 0.018 0.002 PHE C 255 TYR 0.024 0.001 TYR A 179 ARG 0.009 0.001 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 790 MET cc_start: 0.1145 (ptt) cc_final: -0.0007 (ttt) REVERT: B 120 MET cc_start: 0.5013 (mtt) cc_final: 0.4775 (mmm) outliers start: 11 outliers final: 6 residues processed: 87 average time/residue: 0.1979 time to fit residues: 26.5573 Evaluate side-chains 81 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain C residue 226 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.0050 chunk 85 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 0.0670 chunk 32 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10365 Z= 0.205 Angle : 0.567 6.763 14003 Z= 0.288 Chirality : 0.041 0.192 1530 Planarity : 0.004 0.048 1786 Dihedral : 8.404 144.306 1405 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.20 % Allowed : 9.25 % Favored : 89.55 % 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: 0.97 (0.24), residues: 1231 helix: 1.11 (0.22), residues: 598 sheet: 1.04 (0.40), residues: 157 loop : 0.04 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.009 0.001 HIS C 275 PHE 0.020 0.001 PHE A 360 TYR 0.021 0.001 TYR A 179 ARG 0.004 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 TRP cc_start: 0.7586 (m100) cc_final: 0.7357 (m100) REVERT: A 135 MET cc_start: 0.8216 (mmm) cc_final: 0.7857 (mmm) REVERT: A 180 PHE cc_start: 0.8449 (m-80) cc_final: 0.8229 (m-10) REVERT: A 515 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6823 (mtt) REVERT: A 790 MET cc_start: 0.1378 (ptt) cc_final: 0.0292 (ttt) REVERT: B 36 MET cc_start: 0.7683 (mtt) cc_final: 0.7439 (mmt) REVERT: B 120 MET cc_start: 0.5320 (mtt) cc_final: 0.5086 (mmm) outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 0.1981 time to fit residues: 26.5651 Evaluate side-chains 84 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.8980 chunk 1 optimal weight: 0.0770 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10365 Z= 0.255 Angle : 0.566 7.398 14003 Z= 0.288 Chirality : 0.041 0.181 1530 Planarity : 0.004 0.044 1786 Dihedral : 7.665 110.585 1405 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.48 % Allowed : 9.62 % Favored : 88.90 % 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: 1.05 (0.24), residues: 1231 helix: 1.18 (0.22), residues: 603 sheet: 1.09 (0.41), residues: 155 loop : 0.08 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.008 0.001 HIS C 275 PHE 0.019 0.001 PHE A 360 TYR 0.019 0.001 TYR A 179 ARG 0.003 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 76 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8241 (mmm) cc_final: 0.7859 (mmm) REVERT: A 515 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6671 (mtt) REVERT: A 790 MET cc_start: 0.1292 (ptt) cc_final: 0.0215 (ttt) REVERT: B 120 MET cc_start: 0.5183 (mtt) cc_final: 0.4832 (mmm) outliers start: 16 outliers final: 9 residues processed: 88 average time/residue: 0.2251 time to fit residues: 30.3209 Evaluate side-chains 82 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.3980 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10365 Z= 0.289 Angle : 0.589 8.370 14003 Z= 0.299 Chirality : 0.041 0.186 1530 Planarity : 0.004 0.043 1786 Dihedral : 7.608 110.116 1405 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.57 % Allowed : 9.90 % Favored : 88.53 % 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 (0.24), residues: 1231 helix: 1.15 (0.22), residues: 603 sheet: 0.97 (0.41), residues: 156 loop : 0.12 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 79 HIS 0.008 0.001 HIS C 275 PHE 0.018 0.002 PHE A 360 TYR 0.018 0.001 TYR A 179 ARG 0.003 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6644 (mtt) REVERT: A 790 MET cc_start: 0.1342 (ptt) cc_final: 0.0298 (ttt) REVERT: B 120 MET cc_start: 0.5116 (mtt) cc_final: 0.4810 (mmm) outliers start: 17 outliers final: 10 residues processed: 88 average time/residue: 0.1941 time to fit residues: 26.4219 Evaluate side-chains 83 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 138 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10365 Z= 0.215 Angle : 0.566 7.913 14003 Z= 0.284 Chirality : 0.040 0.170 1530 Planarity : 0.004 0.043 1786 Dihedral : 7.139 106.489 1404 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.83 % Allowed : 11.01 % Favored : 88.16 % 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: 1.04 (0.24), residues: 1231 helix: 1.13 (0.22), residues: 608 sheet: 0.78 (0.42), residues: 145 loop : 0.25 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.007 0.001 HIS C 275 PHE 0.022 0.001 PHE B 12 TYR 0.018 0.001 TYR A 179 ARG 0.003 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8075 (mmm) cc_final: 0.7792 (mmm) REVERT: A 515 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6671 (mtt) REVERT: A 648 MET cc_start: 0.8109 (mmm) cc_final: 0.7870 (mmt) REVERT: A 790 MET cc_start: 0.1440 (ptt) cc_final: 0.0397 (ttt) REVERT: B 36 MET cc_start: 0.7406 (mtt) cc_final: 0.7009 (ttm) REVERT: B 120 MET cc_start: 0.5398 (mtt) cc_final: 0.5084 (mmm) REVERT: C 81 ASP cc_start: 0.7290 (m-30) cc_final: 0.7054 (m-30) REVERT: C 325 MET cc_start: 0.8144 (mmt) cc_final: 0.7904 (mmt) outliers start: 9 outliers final: 6 residues processed: 87 average time/residue: 0.2009 time to fit residues: 26.5008 Evaluate side-chains 79 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain B residue 111 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 62.0617 > 50: distance: 27 - 135: 5.171 distance: 30 - 132: 5.901 distance: 40 - 117: 3.215 distance: 43 - 114: 5.213 distance: 56 - 101: 6.602 distance: 59 - 98: 10.488 distance: 73 - 92: 28.896 distance: 83 - 89: 3.972 distance: 89 - 90: 13.631 distance: 90 - 91: 20.009 distance: 91 - 92: 23.905 distance: 91 - 93: 11.856 distance: 93 - 94: 16.858 distance: 94 - 95: 31.294 distance: 94 - 97: 21.253 distance: 95 - 96: 16.891 distance: 95 - 98: 12.968 distance: 98 - 99: 9.595 distance: 99 - 100: 3.072 distance: 99 - 102: 9.222 distance: 100 - 106: 3.181 distance: 102 - 103: 12.316 distance: 103 - 104: 9.993 distance: 103 - 105: 13.478 distance: 107 - 108: 5.422 distance: 111 - 112: 4.651 distance: 112 - 113: 6.975 distance: 116 - 117: 4.736 distance: 118 - 119: 6.168 distance: 119 - 120: 3.280 distance: 120 - 121: 6.832 distance: 121 - 122: 4.671 distance: 122 - 123: 9.140 distance: 122 - 124: 9.092 distance: 125 - 126: 5.402 distance: 126 - 127: 3.272 distance: 127 - 128: 13.331 distance: 129 - 131: 10.420 distance: 132 - 133: 4.906 distance: 133 - 136: 3.958 distance: 134 - 135: 4.180 distance: 137 - 138: 3.608 distance: 137 - 139: 3.029 distance: 138 - 140: 3.361 distance: 139 - 141: 5.247 distance: 140 - 142: 3.152 distance: 141 - 142: 3.896 distance: 142 - 143: 4.736 distance: 146 - 152: 3.020 distance: 149 - 150: 3.432 distance: 149 - 151: 4.924 distance: 152 - 153: 4.001 distance: 153 - 154: 3.895 distance: 153 - 156: 3.898 distance: 154 - 155: 3.054 distance: 156 - 157: 4.283 distance: 157 - 158: 4.751 distance: 157 - 159: 12.274 distance: 161 - 162: 3.307 distance: 162 - 169: 3.853 distance: 164 - 165: 7.958 distance: 165 - 166: 6.360 distance: 166 - 167: 15.144 distance: 166 - 168: 5.221