Starting phenix.real_space_refine on Fri Dec 8 13:04:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/12_2023/8d2x_27153_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/12_2023/8d2x_27153.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/12_2023/8d2x_27153_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/12_2023/8d2x_27153_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/12_2023/8d2x_27153_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/12_2023/8d2x_27153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/12_2023/8d2x_27153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/12_2023/8d2x_27153_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d2x_27153/12_2023/8d2x_27153_updated.pdb" } resolution = 3.4 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= 0.003 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1611 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4465 2.51 5 N 1027 2.21 5 O 1288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6813 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 460, 3404 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 Conformer: "B" Number of residues, atoms: 460, 3404 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 107 bond proxies already assigned to first conformer: 3449 Chain: "B" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1401 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 1416 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1405 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 203, 1405 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 1433 Chain: "A" Number of atoms: 551 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 18, 481 Unusual residues: {'LMT': 13, 'ZGS': 1} Classifications: {'undetermined': 14, 'water': 4} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 18, 481 Unusual residues: {'LMT': 13, 'ZGS': 1} Classifications: {'undetermined': 14, 'water': 4} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 417 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N AARG A 84 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 84 " occ=0.50 residue: pdb=" N AMET A 181 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 181 " occ=0.50 residue: pdb=" N APHE A 396 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 396 " occ=0.50 residue: pdb=" N APHE A 449 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 449 " occ=0.50 residue: pdb=" N AARG C 13 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 13 " occ=0.50 residue: pdb=" C1 ALMT A 604 " occ=0.50 ... (68 atoms not shown) pdb=" O6BBLMT A 604 " occ=0.50 residue: pdb=" C1 ALMT A 613 " occ=0.50 ... (68 atoms not shown) pdb=" O6BBLMT A 613 " occ=0.50 Time building chain proxies: 6.65, per 1000 atoms: 0.98 Number of scatterers: 6813 At special positions: 0 Unit cell: (70.896, 72.584, 141.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1288 8.00 N 1027 7.00 C 4465 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 86 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 93 " distance=2.02 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 186 " distance=2.03 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: 2.53 Conformation dependent library (CDL) restraints added in 2.1 seconds 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1574 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 10 sheets defined 42.2% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 37 through 59 removed outlier: 3.658A pdb=" N GLY A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) Proline residue: A 49 - end of helix Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 73 through 99 removed outlier: 3.654A pdb=" N ASP A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA A 88 " --> pdb=" O AARG A 84 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 110 through 127 Proline residue: A 118 - end of helix removed outlier: 3.519A pdb=" N LEU A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 166 Proline residue: A 158 - end of helix removed outlier: 3.527A pdb=" N ALA A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A 163 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N MET A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 201 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 233 through 261 Processing helix chain 'A' and resid 276 through 287 removed outlier: 4.258A pdb=" N PHE A 279 " --> pdb=" O MET A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 318 removed outlier: 4.939A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.568A pdb=" N LEU A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 350 Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.333A pdb=" N PHE A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 413 Proline residue: A 399 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 420 through 450 Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.663A pdb=" N LEU A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 494 through 506 removed outlier: 5.105A pdb=" N ASN A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'B' and resid 18 through 22 Processing sheet with id= B, first strand: chain 'B' and resid 83 through 88 removed outlier: 5.978A pdb=" N ASN B 36 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LEU B 45 " --> pdb=" O ASN B 36 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 112 through 114 Processing sheet with id= D, first strand: chain 'B' and resid 140 through 145 Processing sheet with id= E, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.544A pdb=" N ALA C 77 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 33 through 36 removed outlier: 3.857A pdb=" N ALA C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 89 through 91 Processing sheet with id= H, first strand: chain 'C' and resid 121 through 123 removed outlier: 5.867A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 164 through 166 removed outlier: 3.744A pdb=" N LEU C 169 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 184 through 187 removed outlier: 4.726A pdb=" N ALA C 184 " --> pdb=" O VAL C 200 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 964 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 990 1.31 - 1.44: 1961 1.44 - 1.56: 3948 1.56 - 1.69: 55 1.69 - 1.81: 46 Bond restraints: 7000 Sorted by residual: bond pdb=" C1B LMT A 612 " pdb=" O5B LMT A 612 " ideal model delta sigma weight residual 1.393 1.523 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C1B LMT A 610 " pdb=" O5B LMT A 610 " ideal model delta sigma weight residual 1.393 1.521 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C1B LMT A 608 " pdb=" O5B LMT A 608 " ideal model delta sigma weight residual 1.393 1.520 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C1BALMT A 613 " pdb=" O5BALMT A 613 " ideal model delta sigma weight residual 1.393 1.518 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C1B LMT A 609 " pdb=" O5B LMT A 609 " ideal model delta sigma weight residual 1.393 1.517 -0.124 2.00e-02 2.50e+03 3.83e+01 ... (remaining 6995 not shown) Histogram of bond angle deviations from ideal: 99.13 - 109.74: 1213 109.74 - 120.36: 5543 120.36 - 130.97: 2755 130.97 - 141.59: 34 141.59 - 152.20: 3 Bond angle restraints: 9548 Sorted by residual: angle pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " pdb=" C06 ZGS A 601 " ideal model delta sigma weight residual 109.50 130.46 -20.96 3.00e+00 1.11e-01 4.88e+01 angle pdb=" C ALA C 193 " pdb=" CA ALA C 193 " pdb=" CB ALA C 193 " ideal model delta sigma weight residual 115.89 110.32 5.57 1.32e+00 5.74e-01 1.78e+01 angle pdb=" C ILE A 211 " pdb=" CA ILE A 211 " pdb=" CB ILE A 211 " ideal model delta sigma weight residual 112.04 107.67 4.37 1.31e+00 5.83e-01 1.11e+01 angle pdb=" C ARG A 455 " pdb=" N GLY A 456 " pdb=" CA GLY A 456 " ideal model delta sigma weight residual 121.41 115.05 6.36 1.96e+00 2.60e-01 1.05e+01 angle pdb=" C GLY B 180 " pdb=" N PRO B 181 " pdb=" CA PRO B 181 " ideal model delta sigma weight residual 121.00 117.28 3.72 1.16e+00 7.43e-01 1.03e+01 ... (remaining 9543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.29: 4071 26.29 - 52.58: 254 52.58 - 78.87: 105 78.87 - 105.16: 101 105.16 - 131.45: 79 Dihedral angle restraints: 4610 sinusoidal: 2138 harmonic: 2472 Sorted by residual: dihedral pdb=" C06 ZGS A 601 " pdb=" C07 ZGS A 601 " pdb=" C08 ZGS A 601 " pdb=" C09 ZGS A 601 " ideal model delta sinusoidal sigma weight residual 77.11 -151.44 -131.45 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C1' LMT A 608 " pdb=" C2' LMT A 608 " pdb=" C3' LMT A 608 " pdb=" O3' LMT A 608 " ideal model delta sinusoidal sigma weight residual -176.68 -60.58 -116.10 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C2B LMT A 611 " pdb=" C1B LMT A 611 " pdb=" O5B LMT A 611 " pdb=" C5B LMT A 611 " ideal model delta sinusoidal sigma weight residual -57.12 58.43 -115.55 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 4607 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 837 0.053 - 0.107: 230 0.107 - 0.160: 73 0.160 - 0.213: 7 0.213 - 0.266: 8 Chirality restraints: 1155 Sorted by residual: chirality pdb=" C1B LMT A 605 " pdb=" C2B LMT A 605 " pdb=" O1B LMT A 605 " pdb=" O5B LMT A 605 " both_signs ideal model delta sigma weight residual False -2.20 -2.47 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C4' LMT A 614 " pdb=" C3' LMT A 614 " pdb=" C5' LMT A 614 " pdb=" O1B LMT A 614 " both_signs ideal model delta sigma weight residual False -2.55 -2.29 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1B LMT A 607 " pdb=" C2B LMT A 607 " pdb=" O1B LMT A 607 " pdb=" O5B LMT A 607 " both_signs ideal model delta sigma weight residual False -2.20 -2.45 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1152 not shown) Planarity restraints: 1135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 204 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C ALA A 204 " -0.053 2.00e-02 2.50e+03 pdb=" O ALA A 204 " 0.020 2.00e-02 2.50e+03 pdb=" N PRO A 205 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP C 46 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO C 47 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 75 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO B 76 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " -0.029 5.00e-02 4.00e+02 ... (remaining 1132 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1544 2.79 - 3.32: 6003 3.32 - 3.84: 11589 3.84 - 4.37: 12613 4.37 - 4.90: 22720 Nonbonded interactions: 54469 Sorted by model distance: nonbonded pdb=" O TYR A 43 " pdb=" OH TYR A 159 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR A 53 " pdb=" OE1 GLN A 152 " model vdw 2.297 2.440 nonbonded pdb=" OD1 ASP A 67 " pdb=" OH TYR A 452 " model vdw 2.308 2.440 nonbonded pdb=" O SER B 30 " pdb=" OG SER B 30 " model vdw 2.343 2.440 nonbonded pdb=" O THR A 381 " pdb=" OG SER A 385 " model vdw 2.344 2.440 ... (remaining 54464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 11.370 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 26.390 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 : 0.012 0.130 7000 Z= 0.752 Angle : 1.290 20.964 9548 Z= 0.538 Chirality : 0.057 0.266 1155 Planarity : 0.007 0.054 1135 Dihedral : 30.615 131.450 3024 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.66 % Favored : 93.22 % Rotamer: Outliers : 0.34 % Allowed : 6.42 % Favored : 93.24 % 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: -1.77 (0.26), residues: 871 helix: 0.18 (0.24), residues: 390 sheet: -0.79 (0.40), residues: 162 loop : -3.13 (0.28), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 106 HIS 0.002 0.001 HIS A 156 PHE 0.021 0.002 PHE B 89 TYR 0.016 0.001 TYR B 48 ARG 0.002 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 0.781 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.1901 time to fit residues: 39.5858 Evaluate side-chains 117 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.600 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 43 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 311 ASN A 324 ASN A 345 GLN B 23 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN C 57 GLN C 171 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7000 Z= 0.285 Angle : 0.902 8.794 9548 Z= 0.382 Chirality : 0.055 0.493 1155 Planarity : 0.005 0.055 1135 Dihedral : 19.206 71.796 1848 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.89 % Allowed : 12.67 % Favored : 83.45 % 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: -1.06 (0.27), residues: 871 helix: 1.10 (0.25), residues: 386 sheet: -0.72 (0.42), residues: 158 loop : -3.02 (0.28), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 103 HIS 0.007 0.002 HIS A 288 PHE 0.016 0.002 PHE B 89 TYR 0.016 0.001 TYR A 251 ARG 0.004 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 0.736 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 135 average time/residue: 0.2072 time to fit residues: 38.3218 Evaluate side-chains 124 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 0.679 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0653 time to fit residues: 2.6951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 21 optimal weight: 0.0370 chunk 78 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 0.7980 chunk 77 optimal weight: 0.0770 chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7000 Z= 0.214 Angle : 0.768 8.301 9548 Z= 0.337 Chirality : 0.047 0.316 1155 Planarity : 0.005 0.052 1135 Dihedral : 12.343 58.302 1848 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.35 % Allowed : 17.06 % Favored : 81.59 % 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: -0.83 (0.28), residues: 871 helix: 1.41 (0.25), residues: 387 sheet: -0.91 (0.40), residues: 163 loop : -2.92 (0.29), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 103 HIS 0.003 0.001 HIS A 288 PHE 0.014 0.002 PHE C 38 TYR 0.013 0.001 TYR A 251 ARG 0.004 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1742 Ramachandran restraints generated. 871 Oldfield, 0 Emsley, 871 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 0.640 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 120 average time/residue: 0.2280 time to fit residues: 36.8700 Evaluate side-chains 107 residues out of total 670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0646 time to fit residues: 1.1527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 65.1214 > 50: distance: 36 - 39: 29.519 distance: 39 - 40: 26.669 distance: 39 - 45: 18.012 distance: 40 - 41: 24.439 distance: 40 - 43: 41.024 distance: 41 - 42: 22.564 distance: 41 - 46: 30.747 distance: 43 - 44: 32.950 distance: 44 - 45: 29.613 distance: 46 - 47: 19.308 distance: 46 - 140: 22.148 distance: 47 - 48: 13.531 distance: 47 - 50: 42.182 distance: 48 - 49: 49.142 distance: 48 - 51: 11.063 distance: 49 - 137: 36.280 distance: 51 - 52: 19.503 distance: 52 - 53: 41.595 distance: 52 - 55: 36.894 distance: 53 - 54: 20.299 distance: 53 - 58: 7.338 distance: 55 - 56: 40.289 distance: 55 - 57: 7.657 distance: 58 - 127: 33.644 distance: 59 - 62: 32.609 distance: 60 - 61: 15.678 distance: 60 - 70: 14.304 distance: 61 - 124: 24.885 distance: 62 - 63: 32.357 distance: 63 - 64: 11.131 distance: 63 - 65: 20.698 distance: 64 - 66: 14.006 distance: 65 - 67: 17.761 distance: 66 - 68: 7.104 distance: 68 - 69: 22.432 distance: 70 - 71: 34.404 distance: 70 - 76: 10.014 distance: 71 - 72: 26.526 distance: 71 - 74: 33.413 distance: 72 - 73: 13.166 distance: 72 - 77: 12.070 distance: 74 - 75: 13.267 distance: 75 - 76: 25.178 distance: 77 - 78: 9.691 distance: 78 - 79: 7.158 distance: 78 - 81: 17.978 distance: 79 - 80: 23.401 distance: 79 - 84: 18.550 distance: 81 - 82: 25.468 distance: 81 - 83: 16.782 distance: 84 - 85: 9.417 distance: 85 - 86: 7.569 distance: 85 - 88: 19.808 distance: 86 - 87: 10.989 distance: 89 - 90: 9.403 distance: 90 - 91: 41.281 distance: 90 - 93: 29.851 distance: 91 - 92: 24.009 distance: 91 - 94: 23.146 distance: 94 - 95: 13.603 distance: 95 - 96: 11.997 distance: 95 - 98: 11.935 distance: 96 - 97: 24.719 distance: 96 - 100: 7.930 distance: 98 - 99: 33.751 distance: 100 - 101: 10.852 distance: 101 - 102: 50.268 distance: 102 - 103: 28.240 distance: 102 - 104: 31.961