Starting phenix.real_space_refine on Sat Dec 9 03:24:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/12_2023/8fgx_29077_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/12_2023/8fgx_29077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/12_2023/8fgx_29077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/12_2023/8fgx_29077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/12_2023/8fgx_29077_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/12_2023/8fgx_29077_trim.pdb" } resolution = 2.62 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 22 5.16 5 C 3186 2.51 5 N 838 2.21 5 O 980 1.98 5 H 4873 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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: 9899 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3252 Classifications: {'peptide': 213} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "B" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3190 Classifications: {'peptide': 216} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 202} Chain breaks: 1 Chain: "C" Number of atoms: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3415 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain breaks: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.71, per 1000 atoms: 0.48 Number of scatterers: 9899 At special positions: 0 Unit cell: (106.683, 99.24, 83.527, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 980 8.00 N 838 7.00 C 3186 6.00 H 4873 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 419 " - pdb=" SG CYS C 435 " distance=2.03 Simple disulfide: pdb=" SG CYS C 517 " - pdb=" SG CYS C 584 " distance=2.03 Simple disulfide: pdb=" SG CYS C 548 " - pdb=" SG CYS C 563 " 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 Links applied NAG-ASN " NAG C 701 " - " ASN C 396 " " NAG C 702 " - " ASN C 453 " " NAG C 703 " - " ASN C 494 " Time building additional restraints: 8.25 Conformation dependent library (CDL) restraints added in 1.2 seconds 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 13 sheets defined 11.3% alpha, 46.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.701A pdb=" N PHE A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.686A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.727A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'C' and resid 432 through 437 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 506 through 511 removed outlier: 3.812A pdb=" N THR C 510 " --> pdb=" O LYS C 507 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER C 511 " --> pdb=" O GLY C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 550 removed outlier: 4.006A pdb=" N LYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 626 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.419A pdb=" N LEU A 11 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 33 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR A 49 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.419A pdb=" N LEU A 11 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 97 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 118 removed outlier: 4.963A pdb=" N SER A 131 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU A 181 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL A 133 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 179 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU A 135 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER A 177 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASN A 137 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 175 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.415A pdb=" N MET B 34 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.684A pdb=" N CYS B 96 " --> pdb=" O TRP B 111 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP B 111 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY B 98 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.061A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.061A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 162 removed outlier: 4.313A pdb=" N TYR B 202 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 405 through 410 removed outlier: 6.903A pdb=" N VAL C 410 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N HIS C 417 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 486 " --> pdb=" O ILE C 469 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE C 469 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS C 488 " --> pdb=" O LYS C 467 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE C 466 " --> pdb=" O TRP C 445 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TRP C 445 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 536 through 539 removed outlier: 3.727A pdb=" N THR C 520 " --> pdb=" O PRO C 581 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU C 582 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N CYS C 563 " --> pdb=" O VAL C 543 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 8.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4858 1.03 - 1.23: 18 1.23 - 1.42: 2174 1.42 - 1.61: 2942 1.61 - 1.81: 29 Bond restraints: 10021 Sorted by residual: bond pdb=" N ILE C 391 " pdb=" CA ILE C 391 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.58e+00 bond pdb=" N ILE C 391 " pdb=" H ILE C 391 " ideal model delta sigma weight residual 0.860 0.888 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C1 NAG C 702 " pdb=" O5 NAG C 702 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.59e+00 bond pdb=" C1 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" C1 NAG C 703 " pdb=" O5 NAG C 703 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.37e+00 ... (remaining 10016 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.71: 173 106.71 - 113.53: 11866 113.53 - 120.35: 2912 120.35 - 127.17: 3013 127.17 - 133.99: 79 Bond angle restraints: 18043 Sorted by residual: angle pdb=" CA PRO C 608 " pdb=" C PRO C 608 " pdb=" N GLY C 609 " ideal model delta sigma weight residual 114.66 116.82 -2.16 1.34e+00 5.57e-01 2.60e+00 angle pdb=" CA ILE C 391 " pdb=" N ILE C 391 " pdb=" H ILE C 391 " ideal model delta sigma weight residual 114.00 109.40 4.60 3.00e+00 1.11e-01 2.35e+00 angle pdb=" N ALA A 51 " pdb=" CA ALA A 51 " pdb=" C ALA A 51 " ideal model delta sigma weight residual 110.80 114.05 -3.25 2.13e+00 2.20e-01 2.33e+00 angle pdb=" N SER C 597 " pdb=" CA SER C 597 " pdb=" C SER C 597 " ideal model delta sigma weight residual 113.18 111.31 1.87 1.33e+00 5.65e-01 1.98e+00 angle pdb=" C TYR A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta sigma weight residual 121.54 124.17 -2.63 1.91e+00 2.74e-01 1.90e+00 ... (remaining 18038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 4465 17.41 - 34.81: 147 34.81 - 52.22: 58 52.22 - 69.62: 26 69.62 - 87.03: 15 Dihedral angle restraints: 4711 sinusoidal: 2501 harmonic: 2210 Sorted by residual: dihedral pdb=" CA ARG A 142 " pdb=" C ARG A 142 " pdb=" N GLU A 143 " pdb=" CA GLU A 143 " ideal model delta harmonic sigma weight residual -180.00 -162.97 -17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA PHE B 95 " pdb=" C PHE B 95 " pdb=" N CYS B 96 " pdb=" CA CYS B 96 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 68.07 24.93 1 1.00e+01 1.00e-02 8.94e+00 ... (remaining 4708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 504 0.033 - 0.065: 187 0.065 - 0.097: 37 0.097 - 0.130: 58 0.130 - 0.162: 2 Chirality restraints: 788 Sorted by residual: chirality pdb=" C1 NAG C 703 " pdb=" ND2 ASN C 494 " pdb=" C2 NAG C 703 " pdb=" O5 NAG C 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA ILE C 531 " pdb=" N ILE C 531 " pdb=" C ILE C 531 " pdb=" CB ILE C 531 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE A 21 " pdb=" N ILE A 21 " pdb=" C ILE A 21 " pdb=" CB ILE A 21 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 785 not shown) Planarity restraints: 1491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 607 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO C 608 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 608 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 608 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 156 " -0.022 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 157 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 209 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO B 210 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " -0.014 5.00e-02 4.00e+02 ... (remaining 1488 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 849 2.22 - 2.82: 21627 2.82 - 3.41: 25899 3.41 - 4.01: 38020 4.01 - 4.60: 56223 Nonbonded interactions: 142618 Sorted by model distance: nonbonded pdb=" OE1 GLU A 123 " pdb=" H GLU A 123 " model vdw 1.630 1.850 nonbonded pdb=" HH TYR A 36 " pdb=" OE1 GLN A 89 " model vdw 1.633 1.850 nonbonded pdb=" O ASP A 82 " pdb=" HH TYR A 86 " model vdw 1.648 1.850 nonbonded pdb="HE22 GLN B 6 " pdb=" O TYR B 94 " model vdw 1.665 1.850 nonbonded pdb=" OE1 GLN C 409 " pdb="HE21 GLN C 415 " model vdw 1.671 1.850 ... (remaining 142613 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 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: 2.120 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: 0.150 Extract box with map and model: 9.380 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 35.610 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: 0.000 Load rotamer database and sin/cos tables:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 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 : 0.003 0.031 5148 Z= 0.184 Angle : 0.446 4.136 7002 Z= 0.230 Chirality : 0.044 0.162 788 Planarity : 0.003 0.041 883 Dihedral : 9.989 87.028 1879 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.41 (0.36), residues: 631 helix: -0.33 (0.92), residues: 33 sheet: 0.66 (0.31), residues: 270 loop : 1.58 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.002 0.001 HIS A 198 PHE 0.010 0.001 PHE A 46 TYR 0.006 0.001 TYR A 91 ARG 0.002 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 3.3076 time to fit residues: 198.3499 Evaluate side-chains 42 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5148 Z= 0.277 Angle : 0.499 4.994 7002 Z= 0.268 Chirality : 0.045 0.154 788 Planarity : 0.004 0.040 883 Dihedral : 5.285 44.800 745 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.36 % Allowed : 6.29 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.36 (0.35), residues: 631 helix: -0.21 (0.83), residues: 33 sheet: 0.65 (0.30), residues: 278 loop : 1.53 (0.39), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 162 HIS 0.002 0.001 HIS A 189 PHE 0.016 0.001 PHE B 95 TYR 0.008 0.001 TYR A 91 ARG 0.004 0.001 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 2.8615 time to fit residues: 128.2301 Evaluate side-chains 39 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2561 time to fit residues: 1.3497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5148 Z= 0.209 Angle : 0.468 4.242 7002 Z= 0.247 Chirality : 0.044 0.146 788 Planarity : 0.003 0.032 883 Dihedral : 4.876 38.711 745 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.54 % Allowed : 6.47 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.41 (0.34), residues: 631 helix: -0.00 (0.83), residues: 33 sheet: 0.71 (0.29), residues: 280 loop : 1.51 (0.39), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.002 0.001 HIS C 434 PHE 0.012 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.003 0.000 ARG C 416 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 41 average time/residue: 2.8422 time to fit residues: 121.7854 Evaluate side-chains 36 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.844 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3303 time to fit residues: 1.4437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5148 Z= 0.216 Angle : 0.469 4.542 7002 Z= 0.247 Chirality : 0.044 0.150 788 Planarity : 0.003 0.032 883 Dihedral : 4.528 31.204 745 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.36 % Allowed : 7.73 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.37 (0.34), residues: 631 helix: -0.08 (0.84), residues: 34 sheet: 0.75 (0.29), residues: 279 loop : 1.43 (0.39), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 162 HIS 0.002 0.001 HIS A 53 PHE 0.011 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.002 0.000 ARG C 560 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 39 average time/residue: 2.6691 time to fit residues: 109.2395 Evaluate side-chains 37 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 54 optimal weight: 0.0670 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5148 Z= 0.249 Angle : 0.474 4.361 7002 Z= 0.250 Chirality : 0.044 0.150 788 Planarity : 0.003 0.032 883 Dihedral : 4.377 27.327 745 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.18 % Allowed : 7.91 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.37 (0.34), residues: 631 helix: -0.01 (0.83), residues: 34 sheet: 0.77 (0.30), residues: 273 loop : 1.39 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 111 HIS 0.002 0.001 HIS A 53 PHE 0.012 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.001 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 2.6329 time to fit residues: 107.6369 Evaluate side-chains 37 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.796 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2583 time to fit residues: 1.3156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5148 Z= 0.221 Angle : 0.473 4.648 7002 Z= 0.249 Chirality : 0.044 0.151 788 Planarity : 0.003 0.033 883 Dihedral : 4.204 24.559 745 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.36 % Allowed : 8.63 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.32 (0.34), residues: 631 helix: -0.11 (0.81), residues: 35 sheet: 0.75 (0.29), residues: 273 loop : 1.34 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 111 HIS 0.002 0.001 HIS A 53 PHE 0.011 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.001 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 2.3834 time to fit residues: 102.6058 Evaluate side-chains 35 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 1.368 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4990 time to fit residues: 2.8117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5148 Z= 0.253 Angle : 0.485 4.571 7002 Z= 0.255 Chirality : 0.044 0.149 788 Planarity : 0.003 0.033 883 Dihedral : 4.163 23.093 745 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.18 % Allowed : 9.35 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.31 (0.34), residues: 631 helix: -0.08 (0.81), residues: 36 sheet: 0.76 (0.29), residues: 273 loop : 1.32 (0.39), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 111 HIS 0.002 0.001 HIS A 53 PHE 0.012 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.001 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 2.4987 time to fit residues: 94.6894 Evaluate side-chains 34 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 71.2468 > 50: distance: 140 - 149: 31.520 distance: 149 - 150: 45.129 distance: 149 - 158: 51.736 distance: 150 - 151: 21.581 distance: 150 - 153: 21.645 distance: 150 - 159: 29.734 distance: 151 - 152: 39.376 distance: 151 - 171: 57.513 distance: 153 - 154: 49.246 distance: 153 - 160: 50.721 distance: 153 - 161: 45.862 distance: 154 - 155: 16.566 distance: 154 - 162: 45.221 distance: 154 - 163: 20.562 distance: 155 - 156: 24.225 distance: 155 - 164: 6.470 distance: 155 - 165: 24.389 distance: 156 - 157: 4.405 distance: 156 - 166: 10.406 distance: 156 - 167: 21.205 distance: 157 - 168: 5.527 distance: 157 - 170: 4.080 distance: 171 - 172: 14.733 distance: 171 - 177: 27.966 distance: 172 - 175: 11.453 distance: 172 - 178: 36.687 distance: 173 - 174: 11.048 distance: 173 - 185: 49.245 distance: 175 - 176: 25.460 distance: 175 - 180: 3.816 distance: 176 - 177: 7.628 distance: 176 - 181: 13.691 distance: 176 - 182: 21.525 distance: 177 - 183: 20.484 distance: 177 - 184: 45.116 distance: 185 - 193: 40.892 distance: 186 - 187: 55.953 distance: 186 - 189: 16.988 distance: 186 - 194: 28.444 distance: 187 - 188: 38.022 distance: 187 - 204: 43.291 distance: 189 - 190: 31.754 distance: 189 - 191: 17.225 distance: 189 - 195: 22.935 distance: 190 - 192: 22.443 distance: 190 - 196: 10.594 distance: 190 - 197: 42.470 distance: 191 - 198: 10.782 distance: 191 - 199: 7.491 distance: 191 - 200: 15.990 distance: 192 - 201: 18.401 distance: 192 - 202: 14.050 distance: 192 - 203: 22.127 distance: 204 - 205: 17.395 distance: 204 - 210: 15.453 distance: 205 - 206: 56.863 distance: 206 - 207: 39.620 distance: 206 - 215: 39.972 distance: 208 - 209: 7.072 distance: 208 - 212: 39.406 distance: 208 - 213: 16.222 distance: 209 - 214: 7.374 distance: 215 - 216: 40.097 distance: 215 - 223: 7.591 distance: 216 - 217: 56.761 distance: 216 - 219: 27.419 distance: 216 - 224: 40.388 distance: 217 - 218: 39.322 distance: 217 - 234: 28.875 distance: 219 - 220: 39.827 distance: 219 - 225: 13.618 distance: 219 - 226: 42.374 distance: 220 - 221: 13.842 distance: 220 - 222: 36.809 distance: 220 - 227: 20.947 distance: 221 - 228: 18.730 distance: 221 - 229: 13.480 distance: 221 - 230: 30.801 distance: 222 - 231: 4.697 distance: 222 - 232: 15.866 distance: 234 - 235: 27.579 distance: 234 - 240: 19.050 distance: 235 - 236: 46.329 distance: 235 - 238: 40.580 distance: 235 - 241: 21.752 distance: 236 - 237: 38.539 distance: 236 - 248: 38.452 distance: 238 - 239: 24.641 distance: 238 - 242: 7.400 distance: 239 - 240: 41.655 distance: 239 - 244: 14.413 distance: 239 - 245: 3.211 distance: 240 - 246: 33.231 distance: 240 - 247: 5.771 distance: 248 - 249: 43.042 distance: 249 - 250: 9.643 distance: 249 - 252: 40.321 distance: 249 - 255: 15.771 distance: 250 - 251: 16.614 distance: 250 - 259: 52.637 distance: 251 - 288: 23.907 distance: 252 - 256: 35.614 distance: 252 - 257: 39.658 distance: 253 - 258: 48.763 distance: 259 - 260: 25.071 distance: 260 - 261: 48.325 distance: 260 - 263: 8.568 distance: 260 - 269: 26.782 distance: 261 - 262: 24.433 distance: 261 - 281: 17.535 distance: 263 - 264: 31.093 distance: 263 - 270: 6.331 distance: 263 - 271: 16.360 distance: 264 - 265: 34.433 distance: 264 - 272: 3.734 distance: 264 - 273: 22.882 distance: 265 - 266: 27.850 distance: 265 - 274: 3.089 distance: 265 - 275: 4.455 distance: 266 - 276: 7.098 distance: 266 - 277: 7.304 distance: 267 - 280: 5.831 distance: 281 - 282: 24.785 distance: 281 - 285: 15.944 distance: 282 - 283: 30.385 distance: 282 - 286: 25.407 distance: 282 - 287: 43.761 distance: 283 - 284: 45.162 distance: 283 - 288: 13.269 distance: 288 - 289: 5.842 distance: 288 - 296: 50.810 distance: 289 - 290: 7.561 distance: 289 - 297: 22.034 distance: 290 - 291: 32.998 distance: 290 - 300: 30.934 distance: 292 - 293: 40.409 distance: 292 - 299: 24.151 distance: 293 - 294: 28.839 distance: 293 - 295: 37.909