Starting phenix.real_space_refine on Fri Jan 19 00:36:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/01_2024/8fgx_29077_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/01_2024/8fgx_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_29077/01_2024/8fgx_29077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/01_2024/8fgx_29077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/01_2024/8fgx_29077_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fgx_29077/01_2024/8fgx_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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 4.61, per 1000 atoms: 0.47 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: 8.40 Conformation dependent library (CDL) restraints added in 1.1 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: 0.98 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: 3.92 Time building geometry restraints manager: 8.64 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: 4489 17.41 - 34.81: 147 34.81 - 52.22: 58 52.22 - 69.62: 26 69.62 - 87.03: 15 Dihedral angle restraints: 4735 sinusoidal: 2525 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 4732 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: 1.760 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: 0.160 Extract box with map and model: 9.510 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 36.850 Find NCS groups from input model: 0.260 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:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.240 ------------------------------------------------------------------------------- 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 : 0.784 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: 3.3241 time to fit residues: 199.3456 Evaluate side-chains 42 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.8872 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5148 Z= 0.270 Angle : 0.494 4.493 7002 Z= 0.265 Chirality : 0.045 0.151 788 Planarity : 0.004 0.036 883 Dihedral : 5.336 45.633 745 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 1.37 (0.35), residues: 631 helix: -0.22 (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 0.007 0.001 TYR A 49 ARG 0.006 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 : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8519 (tt0) cc_final: 0.8197 (tt0) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 2.7944 time to fit residues: 125.3172 Evaluate side-chains 40 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 443 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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: 0.8885 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5148 Z= 0.255 Angle : 0.476 4.509 7002 Z= 0.252 Chirality : 0.044 0.147 788 Planarity : 0.003 0.032 883 Dihedral : 4.844 37.371 745 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.54 % Allowed : 6.65 % Favored : 92.81 % 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: -0.20 (0.81), residues: 34 sheet: 0.69 (0.29), residues: 274 loop : 1.40 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 162 HIS 0.002 0.001 HIS C 417 PHE 0.013 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.003 0.001 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 42 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8512 (tt0) cc_final: 0.8247 (tt0) outliers start: 3 outliers final: 2 residues processed: 39 average time/residue: 2.7520 time to fit residues: 112.2932 Evaluate side-chains 37 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 554 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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: 0.8867 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 0.022 5148 Z= 0.167 Angle : 0.460 4.583 7002 Z= 0.241 Chirality : 0.044 0.151 788 Planarity : 0.003 0.031 883 Dihedral : 4.470 31.047 745 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.18 % Allowed : 7.73 % Favored : 92.09 % 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: -0.14 (0.83), residues: 34 sheet: 0.79 (0.30), residues: 279 loop : 1.45 (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 0.010 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 42 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 2.7796 time to fit residues: 119.6014 Evaluate side-chains 37 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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: 0.8980 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8880 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5148 Z= 0.215 Angle : 0.467 4.059 7002 Z= 0.245 Chirality : 0.044 0.151 788 Planarity : 0.003 0.032 883 Dihedral : 4.333 28.118 745 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.18 % Allowed : 8.09 % Favored : 91.73 % 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: 1.42 (0.34), residues: 631 helix: -0.05 (0.83), residues: 34 sheet: 0.83 (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 0.011 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.001 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 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 39 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8459 (tt0) cc_final: 0.8125 (tt0) outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 2.7230 time to fit residues: 108.3400 Evaluate side-chains 38 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 554 ASP 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: 0.2980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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: 0.8900 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5148 Z= 0.285 Angle : 0.485 4.712 7002 Z= 0.255 Chirality : 0.044 0.149 788 Planarity : 0.003 0.032 883 Dihedral : 4.254 23.984 745 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.54 % Allowed : 8.27 % Favored : 91.19 % 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: -0.12 (0.83), residues: 35 sheet: 0.76 (0.30), residues: 273 loop : 1.32 (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 0.013 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.002 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: 3 poor density : 39 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 2.5172 time to fit residues: 106.0570 Evaluate side-chains 34 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 554 ASP 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: 0.8980 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 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: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.8896 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5148 Z= 0.243 Angle : 0.480 4.630 7002 Z= 0.252 Chirality : 0.044 0.151 788 Planarity : 0.003 0.033 883 Dihedral : 4.160 22.403 745 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: 1.30 (0.34), residues: 631 helix: -0.13 (0.82), residues: 36 sheet: 0.78 (0.29), residues: 273 loop : 1.29 (0.38), 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 36 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 2.4662 time to fit residues: 90.8302 Evaluate side-chains 34 residues out of total 556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 554 ASP 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: 72.1474 > 50: distance: 140 - 149: 34.566 distance: 149 - 150: 39.579 distance: 149 - 158: 69.154 distance: 150 - 151: 40.214 distance: 150 - 153: 55.648 distance: 150 - 159: 40.239 distance: 151 - 152: 38.893 distance: 151 - 171: 40.350 distance: 153 - 154: 40.024 distance: 153 - 160: 57.264 distance: 153 - 161: 56.907 distance: 154 - 155: 55.237 distance: 154 - 162: 56.350 distance: 154 - 163: 40.459 distance: 155 - 156: 56.668 distance: 155 - 164: 39.260 distance: 156 - 157: 44.583 distance: 156 - 166: 40.448 distance: 156 - 167: 56.905 distance: 157 - 168: 24.120 distance: 157 - 169: 23.930 distance: 157 - 170: 22.795 distance: 172 - 173: 57.042 distance: 172 - 175: 40.423 distance: 172 - 178: 39.393 distance: 173 - 185: 56.701 distance: 175 - 179: 40.605 distance: 175 - 180: 39.064 distance: 176 - 177: 39.392 distance: 176 - 182: 39.489 distance: 177 - 183: 40.661 distance: 177 - 184: 39.057 distance: 185 - 193: 39.108 distance: 186 - 187: 56.064 distance: 186 - 194: 57.292 distance: 187 - 188: 40.963 distance: 187 - 204: 39.776 distance: 189 - 190: 57.601 distance: 189 - 191: 39.203 distance: 189 - 195: 40.818 distance: 190 - 196: 55.679 distance: 190 - 197: 39.547 distance: 191 - 199: 39.431 distance: 192 - 201: 39.382 distance: 192 - 203: 40.415 distance: 205 - 206: 56.266 distance: 206 - 207: 57.172 distance: 208 - 209: 38.148 distance: 209 - 214: 40.284 distance: 215 - 223: 39.383 distance: 216 - 217: 56.371 distance: 216 - 219: 39.690 distance: 216 - 224: 56.433 distance: 217 - 218: 40.670 distance: 219 - 220: 40.438 distance: 219 - 226: 39.429 distance: 220 - 227: 39.682 distance: 221 - 228: 40.196 distance: 221 - 229: 40.401 distance: 221 - 230: 39.673 distance: 222 - 232: 39.138 distance: 235 - 236: 56.522 distance: 235 - 238: 39.453 distance: 235 - 241: 40.485 distance: 236 - 237: 57.589 distance: 236 - 248: 39.191 distance: 239 - 240: 40.305 distance: 239 - 244: 33.031 distance: 239 - 245: 39.271 distance: 240 - 246: 39.814 distance: 248 - 249: 39.557 distance: 249 - 252: 70.432 distance: 250 - 259: 39.631 distance: 251 - 288: 59.158 distance: 252 - 253: 39.576 distance: 252 - 256: 56.756 distance: 253 - 258: 56.770 distance: 259 - 260: 40.868 distance: 259 - 268: 40.037 distance: 260 - 263: 39.615 distance: 261 - 262: 40.024 distance: 261 - 281: 39.784 distance: 263 - 271: 9.549 distance: 264 - 265: 55.129 distance: 264 - 272: 39.726 distance: 264 - 273: 40.913 distance: 265 - 266: 41.175 distance: 266 - 277: 52.001 distance: 267 - 279: 19.877 distance: 282 - 283: 68.811 distance: 282 - 286: 40.662 distance: 282 - 287: 69.239 distance: 283 - 284: 55.858 distance: 288 - 289: 41.372 distance: 288 - 296: 40.108 distance: 289 - 290: 39.953 distance: 290 - 300: 34.534 distance: 292 - 293: 39.764 distance: 293 - 294: 39.863 distance: 293 - 295: 40.036