Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 23:33:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unl_26626/10_2023/7unl_26626.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unl_26626/10_2023/7unl_26626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unl_26626/10_2023/7unl_26626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unl_26626/10_2023/7unl_26626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unl_26626/10_2023/7unl_26626.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unl_26626/10_2023/7unl_26626.pdb" } resolution = 2.45 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 8 8.98 5 S 38 5.16 5 C 3754 2.51 5 N 938 2.21 5 O 1086 1.98 5 H 5900 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 11724 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5798 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5798 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Time building chain proxies: 5.70, per 1000 atoms: 0.49 Number of scatterers: 11724 At special positions: 0 Unit cell: (104.55, 70.55, 78.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 8 19.00 S 38 16.00 O 1086 8.00 N 938 7.00 C 3754 6.00 H 5900 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.14 Conformation dependent library (CDL) restraints added in 1.0 seconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 89.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 33 through 49 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 66 through 102 Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 137 through 164 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 257 through 284 removed outlier: 5.037A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 306 through 332 removed outlier: 3.565A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 368 through 399 removed outlier: 3.711A pdb=" N GLU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 4.932A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 3.522A pdb=" N CYS A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 461 removed outlier: 4.520A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'B' and resid 33 through 49 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 66 through 102 Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 137 through 164 Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 257 through 284 removed outlier: 5.036A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.566A pdb=" N PHE B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 368 through 399 removed outlier: 3.710A pdb=" N GLU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 4.932A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 3.523A pdb=" N CYS B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 461 removed outlier: 4.521A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 476 466 hydrogen bonds defined for protein. 1368 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: 4.18 Time building geometry restraints manager: 11.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5882 1.03 - 1.22: 18 1.22 - 1.42: 2382 1.42 - 1.61: 3390 1.61 - 1.81: 58 Bond restraints: 11730 Sorted by residual: bond pdb=" CD1 PHE B 314 " pdb=" HD1 PHE B 314 " ideal model delta sigma weight residual 0.930 0.965 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C THR B 306 " pdb=" N GLY B 307 " ideal model delta sigma weight residual 1.340 1.329 0.011 6.60e-03 2.30e+04 2.64e+00 bond pdb=" C THR A 306 " pdb=" N GLY A 307 " ideal model delta sigma weight residual 1.340 1.329 0.011 6.60e-03 2.30e+04 2.64e+00 bond pdb=" NE2 GLN A 34 " pdb="HE21 GLN A 34 " ideal model delta sigma weight residual 0.860 0.831 0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" CE1 PHE B 314 " pdb=" HE1 PHE B 314 " ideal model delta sigma weight residual 0.930 0.904 0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 11725 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.83: 206 106.83 - 113.64: 13990 113.64 - 120.44: 3984 120.44 - 127.24: 3017 127.24 - 134.05: 67 Bond angle restraints: 21264 Sorted by residual: angle pdb=" CA GLN A 34 " pdb=" CB GLN A 34 " pdb=" CG GLN A 34 " ideal model delta sigma weight residual 114.10 119.78 -5.68 2.00e+00 2.50e-01 8.06e+00 angle pdb=" CA GLN B 34 " pdb=" CB GLN B 34 " pdb=" CG GLN B 34 " ideal model delta sigma weight residual 114.10 119.77 -5.67 2.00e+00 2.50e-01 8.02e+00 angle pdb=" N PHE A 314 " pdb=" CA PHE A 314 " pdb=" CB PHE A 314 " ideal model delta sigma weight residual 109.72 105.67 4.05 1.70e+00 3.46e-01 5.67e+00 angle pdb=" N PHE B 314 " pdb=" CA PHE B 314 " pdb=" CB PHE B 314 " ideal model delta sigma weight residual 109.72 105.76 3.96 1.70e+00 3.46e-01 5.44e+00 angle pdb=" C GLN B 34 " pdb=" CA GLN B 34 " pdb=" CB GLN B 34 " ideal model delta sigma weight residual 110.88 114.45 -3.57 1.57e+00 4.06e-01 5.17e+00 ... (remaining 21259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4301 17.53 - 35.05: 337 35.05 - 52.58: 78 52.58 - 70.11: 14 70.11 - 87.63: 4 Dihedral angle restraints: 4734 sinusoidal: 2142 harmonic: 2592 Sorted by residual: dihedral pdb=" CA PHE A 99 " pdb=" C PHE A 99 " pdb=" N GLN A 100 " pdb=" CA GLN A 100 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE B 99 " pdb=" C PHE B 99 " pdb=" N GLN B 100 " pdb=" CA GLN B 100 " ideal model delta harmonic sigma weight residual 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ASP A 283 " pdb=" C ASP A 283 " pdb=" N ASN A 284 " pdb=" CA ASN A 284 " ideal model delta harmonic sigma weight residual -180.00 -161.22 -18.78 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 4731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 581 0.026 - 0.051: 242 0.051 - 0.077: 94 0.077 - 0.103: 48 0.103 - 0.129: 13 Chirality restraints: 978 Sorted by residual: chirality pdb=" CA VAL A 285 " pdb=" N VAL A 285 " pdb=" C VAL A 285 " pdb=" CB VAL A 285 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA VAL B 285 " pdb=" N VAL B 285 " pdb=" C VAL B 285 " pdb=" CB VAL B 285 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA VAL B 136 " pdb=" N VAL B 136 " pdb=" C VAL B 136 " pdb=" CB VAL B 136 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 975 not shown) Planarity restraints: 1672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 314 " 0.026 2.00e-02 2.50e+03 2.83e-02 2.41e+01 pdb=" CG PHE A 314 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 314 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 PHE A 314 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 314 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 314 " -0.036 2.00e-02 2.50e+03 pdb=" CZ PHE A 314 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE A 314 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 PHE A 314 " 0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE A 314 " -0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE A 314 " 0.027 2.00e-02 2.50e+03 pdb=" HZ PHE A 314 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 314 " 0.000 2.00e-02 2.50e+03 2.20e-02 1.45e+01 pdb=" CG PHE B 314 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE B 314 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 314 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 314 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 314 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 314 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE B 314 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 PHE B 314 " 0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE B 314 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE B 314 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE B 314 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 133 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 134 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 134 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 134 " -0.022 5.00e-02 4.00e+02 ... (remaining 1669 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.19: 570 2.19 - 2.92: 30654 2.92 - 3.66: 44464 3.66 - 4.40: 68468 4.40 - 5.14: 107342 Nonbonded interactions: 251498 Sorted by model distance: nonbonded pdb=" OE1 GLU A 259 " pdb=" H GLU A 259 " model vdw 1.448 1.850 nonbonded pdb=" OE1 GLU B 259 " pdb=" H GLU B 259 " model vdw 1.449 1.850 nonbonded pdb=" HG SER A 45 " pdb=" O HOH A 802 " model vdw 1.657 1.850 nonbonded pdb=" HG SER B 45 " pdb=" O HOH B 802 " model vdw 1.659 1.850 nonbonded pdb=" O PHE A 434 " pdb=" HG1 THR A 437 " model vdw 1.660 1.850 ... (remaining 251493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 476 or resid 701 through 703)) selection = chain 'B' } 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: 3.250 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: 0.200 Extract box with map and model: 11.990 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 44.340 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 0.036 5830 Z= 0.226 Angle : 0.559 5.676 7946 Z= 0.319 Chirality : 0.037 0.129 978 Planarity : 0.004 0.039 974 Dihedral : 14.663 87.635 2034 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.94 % Allowed : 8.74 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.34), residues: 726 helix: 1.58 (0.22), residues: 608 sheet: None (None), residues: 0 loop : 1.68 (0.72), residues: 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 99 average time/residue: 2.2123 time to fit residues: 231.2254 Evaluate side-chains 68 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.942 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.1590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5830 Z= 0.238 Angle : 0.523 4.840 7946 Z= 0.276 Chirality : 0.036 0.132 978 Planarity : 0.004 0.031 974 Dihedral : 4.180 25.066 780 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 1.62 % Allowed : 13.43 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.33), residues: 726 helix: 2.51 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.92 (0.74), residues: 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 0.851 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 82 average time/residue: 2.3848 time to fit residues: 205.7912 Evaluate side-chains 64 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 1.1574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5830 Z= 0.275 Angle : 0.522 4.534 7946 Z= 0.276 Chirality : 0.037 0.128 978 Planarity : 0.004 0.029 974 Dihedral : 4.042 24.924 780 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.46 % Allowed : 13.11 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.33), residues: 726 helix: 2.66 (0.22), residues: 610 sheet: None (None), residues: 0 loop : 1.83 (0.73), residues: 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.893 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 2.2384 time to fit residues: 174.9616 Evaluate side-chains 65 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.1570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 5830 Z= 0.252 Angle : 0.498 4.514 7946 Z= 0.261 Chirality : 0.037 0.127 978 Planarity : 0.003 0.028 974 Dihedral : 3.966 24.496 780 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 2.10 % Allowed : 11.81 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.90 (0.33), residues: 726 helix: 2.77 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.53 (0.70), residues: 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.869 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 69 average time/residue: 2.2921 time to fit residues: 167.1845 Evaluate side-chains 66 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.1003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5830 Z= 0.273 Angle : 0.497 4.480 7946 Z= 0.260 Chirality : 0.037 0.127 978 Planarity : 0.003 0.026 974 Dihedral : 3.929 24.141 780 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.43 % Allowed : 12.30 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.93 (0.32), residues: 726 helix: 2.82 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.38 (0.69), residues: 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 1.009 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 72 average time/residue: 2.4983 time to fit residues: 189.1194 Evaluate side-chains 62 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.0527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5830 Z= 0.230 Angle : 0.497 4.416 7946 Z= 0.259 Chirality : 0.036 0.128 978 Planarity : 0.003 0.024 974 Dihedral : 3.898 23.848 780 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.62 % Allowed : 13.43 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.32), residues: 726 helix: 2.90 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.44 (0.69), residues: 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.898 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 2.4979 time to fit residues: 165.5813 Evaluate side-chains 61 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.1942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 50 optimal weight: 0.3980 chunk 58 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5830 Z= 0.199 Angle : 0.478 4.364 7946 Z= 0.249 Chirality : 0.035 0.126 978 Planarity : 0.003 0.026 974 Dihedral : 3.859 23.401 780 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.10 % Allowed : 12.78 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.22 (0.32), residues: 726 helix: 3.03 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.45 (0.68), residues: 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.970 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 63 average time/residue: 2.5266 time to fit residues: 167.4321 Evaluate side-chains 64 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.990 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 2 average time/residue: 0.3860 time to fit residues: 2.0813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN B 361 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5830 Z= 0.207 Angle : 0.489 4.892 7946 Z= 0.254 Chirality : 0.036 0.128 978 Planarity : 0.003 0.025 974 Dihedral : 3.830 23.131 780 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.62 % Allowed : 13.43 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.28 (0.32), residues: 726 helix: 3.06 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.50 (0.67), residues: 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.954 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 66 average time/residue: 2.5445 time to fit residues: 176.4124 Evaluate side-chains 65 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.4096 time to fit residues: 2.1414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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: 70.5911 > 50: distance: 145 - 188: 15.047 distance: 160 - 209: 22.187 distance: 166 - 226: 6.690 distance: 180 - 188: 13.304 distance: 181 - 243: 19.980 distance: 188 - 189: 12.504 distance: 188 - 200: 27.061 distance: 189 - 190: 42.752 distance: 189 - 192: 31.175 distance: 189 - 201: 47.109 distance: 190 - 191: 6.017 distance: 190 - 209: 43.306 distance: 192 - 193: 10.158 distance: 192 - 202: 27.690 distance: 192 - 203: 15.890 distance: 193 - 194: 17.023 distance: 193 - 195: 13.161 distance: 194 - 196: 13.425 distance: 194 - 204: 7.449 distance: 195 - 197: 12.310 distance: 195 - 205: 4.999 distance: 196 - 198: 14.619 distance: 196 - 206: 8.049 distance: 197 - 198: 6.931 distance: 197 - 207: 8.008 distance: 198 - 199: 6.922 distance: 199 - 208: 12.981 distance: 209 - 210: 35.899 distance: 209 - 218: 21.255 distance: 210 - 211: 29.497 distance: 210 - 213: 27.285 distance: 210 - 219: 8.208 distance: 211 - 212: 26.972 distance: 211 - 226: 25.932 distance: 213 - 214: 12.850 distance: 213 - 220: 24.757 distance: 213 - 221: 21.739 distance: 214 - 215: 42.416 distance: 214 - 222: 15.020 distance: 214 - 223: 36.708 distance: 215 - 216: 10.804 distance: 215 - 217: 14.781 distance: 217 - 224: 21.302 distance: 217 - 225: 13.188 distance: 226 - 227: 5.267 distance: 226 - 235: 34.059 distance: 227 - 228: 21.273 distance: 227 - 230: 6.900 distance: 227 - 236: 27.418 distance: 228 - 229: 48.760 distance: 228 - 243: 5.436 distance: 230 - 231: 18.155 distance: 230 - 237: 14.799 distance: 230 - 238: 18.658 distance: 231 - 232: 15.854 distance: 231 - 239: 8.516 distance: 231 - 240: 38.209 distance: 232 - 233: 17.176 distance: 232 - 234: 7.013 distance: 234 - 241: 17.986 distance: 234 - 242: 7.160 distance: 243 - 244: 11.193 distance: 243 - 250: 17.439 distance: 244 - 245: 3.481 distance: 244 - 247: 44.072 distance: 244 - 251: 37.394 distance: 245 - 246: 9.370 distance: 245 - 257: 24.393 distance: 247 - 248: 40.546 distance: 247 - 249: 18.651 distance: 247 - 252: 27.070 distance: 248 - 253: 3.502 distance: 249 - 254: 24.233 distance: 249 - 255: 20.584 distance: 249 - 256: 18.884 distance: 257 - 258: 25.292 distance: 257 - 263: 42.985 distance: 258 - 259: 69.052 distance: 258 - 264: 40.591 distance: 259 - 268: 55.300 distance: 261 - 262: 39.806 distance: 262 - 267: 39.739 distance: 268 - 269: 42.883 distance: 269 - 270: 38.228 distance: 269 - 272: 20.860 distance: 269 - 274: 20.022 distance: 270 - 271: 49.289 distance: 272 - 275: 3.649 distance: 272 - 276: 3.534 distance: 272 - 277: 34.733 distance: 278 - 279: 8.088 distance: 278 - 289: 8.774 distance: 279 - 280: 26.538 distance: 279 - 282: 25.794 distance: 279 - 290: 25.744 distance: 280 - 281: 3.110 distance: 280 - 298: 4.420 distance: 282 - 283: 3.826 distance: 282 - 291: 43.855 distance: 282 - 292: 11.973 distance: 283 - 284: 37.674 distance: 283 - 285: 11.542 distance: 285 - 287: 9.108 distance: 285 - 294: 4.120 distance: 286 - 288: 14.630 distance: 287 - 288: 33.671 distance: 287 - 296: 21.415 distance: 288 - 297: 23.623 distance: 298 - 299: 31.690 distance: 298 - 303: 17.075 distance: 299 - 300: 20.079 distance: 299 - 302: 41.616 distance: 299 - 304: 19.084 distance: 300 - 301: 26.454 distance: 300 - 308: 15.929 distance: 302 - 305: 39.122 distance: 308 - 309: 41.767 distance: 308 - 319: 39.403 distance: 309 - 310: 12.906 distance: 309 - 312: 33.849 distance: 309 - 320: 43.541 distance: 310 - 311: 40.495 distance: 312 - 313: 27.985 distance: 312 - 321: 55.847 distance: 312 - 322: 32.014 distance: 313 - 314: 56.989 distance: 313 - 323: 28.065 distance: 313 - 324: 21.785 distance: 314 - 325: 7.889 distance: 315 - 327: 24.248 distance: 317 - 328: 18.045 distance: 317 - 329: 18.397 distance: 318 - 330: 6.274 distance: 318 - 331: 10.538 distance: 332 - 341: 67.180 distance: 333 - 334: 39.958 distance: 333 - 342: 55.947 distance: 334 - 335: 57.265 distance: 334 - 349: 31.336 distance: 336 - 337: 57.459 distance: 336 - 343: 21.954 distance: 336 - 344: 40.815 distance: 337 - 338: 10.462 distance: 337 - 345: 42.004 distance: 338 - 339: 26.299 distance: 338 - 340: 28.593 distance: 340 - 347: 19.248 distance: 340 - 348: 10.995