Starting phenix.real_space_refine on Thu Dec 7 22:56:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/12_2023/8cpe_16780.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/12_2023/8cpe_16780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/12_2023/8cpe_16780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/12_2023/8cpe_16780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/12_2023/8cpe_16780.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cpe_16780/12_2023/8cpe_16780.pdb" } resolution = 4.0 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= 0.002 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 15 5.16 5 C 1795 2.51 5 N 470 2.21 5 O 625 1.98 5 H 2615 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5520 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1104 Classifications: {'peptide': 77} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Chain: "A" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1104 Classifications: {'peptide': 77} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Chain: "B" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1104 Classifications: {'peptide': 77} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Chain: "D" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1104 Classifications: {'peptide': 77} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Chain: "E" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1104 Classifications: {'peptide': 77} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain breaks: 1 Time building chain proxies: 3.11, per 1000 atoms: 0.56 Number of scatterers: 5520 At special positions: 0 Unit cell: (81.5308, 64.7779, 44.6744, 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 15 16.00 O 625 8.00 N 470 7.00 C 1795 6.00 H 2615 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 91 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 91 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 91 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 91 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 91 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 768.0 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 50.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 6.335A pdb=" N MET A 3 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N MET C 3 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N MET D 3 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.578A pdb=" N VAL A 10 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL C 10 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL D 10 " --> pdb=" O SER E 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.186A pdb=" N THR A 19 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N THR C 19 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR D 19 " --> pdb=" O ILE E 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.423A pdb=" N ALA A 27 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER C 28 " --> pdb=" O ILE B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.556A pdb=" N TYR C 33 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 74 removed outlier: 6.172A pdb=" N ILE A 67 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N SER B 70 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N SER A 69 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN B 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N SER A 71 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA B 74 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER A 73 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 71 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE C 67 " --> pdb=" O ASP D 68 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N SER D 70 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER C 69 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN D 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N SER C 71 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA D 74 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER C 73 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE D 67 " --> pdb=" O ASP E 68 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER E 70 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N SER D 69 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN E 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N SER D 71 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA E 74 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER D 73 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 77 through 78 removed outlier: 6.645A pdb=" N THR C 77 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 81 through 99 removed outlier: 3.625A pdb=" N ASP A 85 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LYS C 82 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ASP B 85 " --> pdb=" O LYS C 82 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLU C 84 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ALA B 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU C 86 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N TYR B 89 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASP C 88 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N CYS B 91 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR C 90 " --> pdb=" O CYS B 91 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N SER B 93 " --> pdb=" O TYR C 90 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN C 92 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASP B 95 " --> pdb=" O GLN C 92 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N TYR C 94 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ASN B 97 " --> pdb=" O TYR C 94 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLY C 96 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N HIS B 99 " --> pdb=" O GLY C 96 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN C 98 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 85 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP D 85 " --> pdb=" O GLU E 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 102 through 104 removed outlier: 6.483A pdb=" N GLY C 103 " --> pdb=" O GLY B 104 " (cutoff:3.500A) 83 hydrogen bonds defined for protein. 249 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 4.08 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: 2615 1.03 - 1.23: 5 1.23 - 1.42: 1375 1.42 - 1.62: 1575 1.62 - 1.82: 20 Bond restraints: 5590 Sorted by residual: bond pdb=" CA GLY E 104 " pdb=" C GLY E 104 " ideal model delta sigma weight residual 1.520 1.513 0.007 7.30e-03 1.88e+04 8.68e-01 bond pdb=" CA GLY B 104 " pdb=" C GLY B 104 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 7.76e-01 bond pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 1.520 1.514 0.006 7.30e-03 1.88e+04 7.19e-01 bond pdb=" CG TYR B 33 " pdb=" CD1 TYR B 33 " ideal model delta sigma weight residual 1.389 1.375 0.014 2.10e-02 2.27e+03 4.26e-01 bond pdb=" CA THR B 17 " pdb=" HA THR B 17 " ideal model delta sigma weight residual 0.970 0.958 0.012 2.00e-02 2.50e+03 3.54e-01 ... (remaining 5585 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.86: 124 106.86 - 113.65: 6300 113.65 - 120.44: 1732 120.44 - 127.23: 1729 127.23 - 134.02: 50 Bond angle restraints: 9935 Sorted by residual: angle pdb=" N ASN E 97 " pdb=" CA ASN E 97 " pdb=" C ASN E 97 " ideal model delta sigma weight residual 107.62 100.11 7.51 1.97e+00 2.58e-01 1.45e+01 angle pdb=" N ASN A 97 " pdb=" CA ASN A 97 " pdb=" C ASN A 97 " ideal model delta sigma weight residual 107.62 100.18 7.44 1.97e+00 2.58e-01 1.43e+01 angle pdb=" N ASN B 97 " pdb=" CA ASN B 97 " pdb=" C ASN B 97 " ideal model delta sigma weight residual 107.62 100.24 7.38 1.97e+00 2.58e-01 1.40e+01 angle pdb=" N ASN D 97 " pdb=" CA ASN D 97 " pdb=" C ASN D 97 " ideal model delta sigma weight residual 107.62 100.25 7.37 1.97e+00 2.58e-01 1.40e+01 angle pdb=" N ASN C 97 " pdb=" CA ASN C 97 " pdb=" C ASN C 97 " ideal model delta sigma weight residual 107.62 100.27 7.35 1.97e+00 2.58e-01 1.39e+01 ... (remaining 9930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.51: 2355 13.51 - 27.01: 190 27.01 - 40.52: 70 40.52 - 54.02: 20 54.02 - 67.53: 20 Dihedral angle restraints: 2655 sinusoidal: 1300 harmonic: 1355 Sorted by residual: dihedral pdb=" CA GLY D 15 " pdb=" C GLY D 15 " pdb=" N LYS D 16 " pdb=" CA LYS D 16 " ideal model delta harmonic sigma weight residual 180.00 151.05 28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA GLY E 15 " pdb=" C GLY E 15 " pdb=" N LYS E 16 " pdb=" CA LYS E 16 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA GLY B 15 " pdb=" C GLY B 15 " pdb=" N LYS B 16 " pdb=" CA LYS B 16 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 2652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 202 0.032 - 0.063: 110 0.063 - 0.095: 72 0.095 - 0.127: 32 0.127 - 0.158: 19 Chirality restraints: 435 Sorted by residual: chirality pdb=" CA ILE B 20 " pdb=" N ILE B 20 " pdb=" C ILE B 20 " pdb=" CB ILE B 20 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE E 20 " pdb=" N ILE E 20 " pdb=" C ILE E 20 " pdb=" CB ILE E 20 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE D 20 " pdb=" N ILE D 20 " pdb=" C ILE D 20 " pdb=" CB ILE D 20 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 432 not shown) Planarity restraints: 880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 102 " -0.001 2.00e-02 2.50e+03 2.22e-02 1.48e+01 pdb=" CG PHE C 102 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE C 102 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 102 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 102 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE C 102 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 102 " -0.008 2.00e-02 2.50e+03 pdb=" HD1 PHE C 102 " 0.034 2.00e-02 2.50e+03 pdb=" HD2 PHE C 102 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 PHE C 102 " -0.017 2.00e-02 2.50e+03 pdb=" HE2 PHE C 102 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE C 102 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 102 " -0.001 2.00e-02 2.50e+03 2.22e-02 1.48e+01 pdb=" CG PHE B 102 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE B 102 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 102 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 102 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE B 102 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 102 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 PHE B 102 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE B 102 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 PHE B 102 " -0.017 2.00e-02 2.50e+03 pdb=" HE2 PHE B 102 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE B 102 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 102 " 0.000 2.00e-02 2.50e+03 2.21e-02 1.47e+01 pdb=" CG PHE A 102 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 102 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 102 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 102 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 102 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 102 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 PHE A 102 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE A 102 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 PHE A 102 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 PHE A 102 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 102 " 0.009 2.00e-02 2.50e+03 ... (remaining 877 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 144 2.11 - 2.73: 9149 2.73 - 3.35: 13555 3.35 - 3.98: 18395 3.98 - 4.60: 27655 Nonbonded interactions: 68898 Sorted by model distance: nonbonded pdb=" OD1 ASN A 1 " pdb=" HG SER B 26 " model vdw 1.485 1.850 nonbonded pdb=" HG SER C 26 " pdb=" OD1 ASN B 1 " model vdw 1.493 1.850 nonbonded pdb=" OD1 ASN C 1 " pdb=" HG SER D 26 " model vdw 1.500 1.850 nonbonded pdb=" OD1 ASN D 1 " pdb=" HG SER E 26 " model vdw 1.501 1.850 nonbonded pdb=" OE1 GLN B 92 " pdb=" HH TYR B 94 " model vdw 1.526 1.850 ... (remaining 68893 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.080 Extract box with map and model: 3.500 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 22.130 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 : 0.002 0.019 2975 Z= 0.171 Angle : 0.932 8.136 4040 Z= 0.532 Chirality : 0.059 0.158 435 Planarity : 0.005 0.023 515 Dihedral : 12.165 49.684 990 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 (0.28), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.006 TRP A 36 HIS 0.014 0.004 HIS B 32 PHE 0.044 0.010 PHE C 102 TYR 0.047 0.007 TYR D 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.530 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1614 time to fit residues: 12.8470 Evaluate side-chains 25 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 0.0980 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 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: 0.7199 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2975 Z= 0.206 Angle : 0.585 4.549 4040 Z= 0.326 Chirality : 0.048 0.131 435 Planarity : 0.003 0.023 515 Dihedral : 7.710 23.258 400 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.52 % Allowed : 10.61 % Favored : 87.88 % 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: -3.63 (0.30), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.23), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 36 HIS 0.003 0.001 HIS A 99 PHE 0.009 0.002 PHE A 2 TYR 0.011 0.001 TYR B 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 0.466 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 33 average time/residue: 0.1594 time to fit residues: 7.5674 Evaluate side-chains 26 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.453 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0664 time to fit residues: 0.7645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2975 Z= 0.192 Angle : 0.567 4.833 4040 Z= 0.314 Chirality : 0.048 0.138 435 Planarity : 0.003 0.020 515 Dihedral : 7.306 20.620 400 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.12 % Allowed : 14.55 % Favored : 83.33 % 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: -3.78 (0.29), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.22), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 100 HIS 0.003 0.001 HIS A 99 PHE 0.012 0.002 PHE B 102 TYR 0.009 0.001 TYR D 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.415 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 29 average time/residue: 0.1482 time to fit residues: 6.3091 Evaluate side-chains 25 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0992 time to fit residues: 0.9548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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: 0.7324 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2975 Z= 0.192 Angle : 0.555 5.229 4040 Z= 0.305 Chirality : 0.048 0.127 435 Planarity : 0.003 0.019 515 Dihedral : 6.957 20.130 400 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.42 % Allowed : 16.67 % Favored : 80.91 % 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: -3.86 (0.29), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.22), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 100 HIS 0.002 0.001 HIS A 99 PHE 0.013 0.002 PHE B 102 TYR 0.007 0.001 TYR A 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 24 time to evaluate : 0.425 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 30 average time/residue: 0.1575 time to fit residues: 6.9306 Evaluate side-chains 24 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.425 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0747 time to fit residues: 0.7549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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: 0.7413 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2975 Z= 0.256 Angle : 0.597 5.765 4040 Z= 0.327 Chirality : 0.048 0.135 435 Planarity : 0.003 0.021 515 Dihedral : 7.064 21.207 400 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 2.42 % Allowed : 16.67 % Favored : 80.91 % 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: -4.14 (0.28), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 100 HIS 0.002 0.000 HIS A 99 PHE 0.010 0.002 PHE B 102 TYR 0.008 0.001 TYR A 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 24 time to evaluate : 0.508 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 30 average time/residue: 0.1790 time to fit residues: 7.7166 Evaluate side-chains 26 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0734 time to fit residues: 0.9975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.0030 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- 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: 0.7454 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2975 Z= 0.230 Angle : 0.594 5.900 4040 Z= 0.325 Chirality : 0.048 0.131 435 Planarity : 0.003 0.022 515 Dihedral : 6.915 20.524 400 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 1.52 % Allowed : 18.18 % Favored : 80.30 % 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: -4.35 (0.27), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.21), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 100 HIS 0.002 0.001 HIS B 32 PHE 0.009 0.002 PHE A 102 TYR 0.006 0.001 TYR A 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 31 average time/residue: 0.2012 time to fit residues: 8.2617 Evaluate side-chains 24 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.458 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0656 time to fit residues: 0.7847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4937 > 50: distance: 26 - 332: 37.747 distance: 29 - 356: 28.912 distance: 148 - 461: 29.382 distance: 320 - 329: 22.281 distance: 329 - 330: 18.068 distance: 329 - 336: 19.042 distance: 330 - 331: 43.637 distance: 330 - 333: 21.617 distance: 330 - 337: 35.456 distance: 331 - 332: 41.429 distance: 331 - 345: 47.560 distance: 333 - 334: 51.139 distance: 333 - 335: 46.874 distance: 333 - 338: 23.309 distance: 334 - 339: 13.167 distance: 334 - 341: 56.268 distance: 335 - 342: 40.252 distance: 335 - 343: 40.071 distance: 335 - 344: 55.252 distance: 345 - 346: 41.749 distance: 345 - 351: 56.896 distance: 346 - 347: 43.838 distance: 346 - 349: 23.166 distance: 346 - 352: 35.253 distance: 347 - 348: 18.680 distance: 347 - 356: 30.724 distance: 349 - 353: 17.789 distance: 349 - 354: 9.726 distance: 350 - 355: 40.408 distance: 356 - 357: 35.693 distance: 356 - 365: 15.106 distance: 357 - 358: 37.976 distance: 357 - 360: 46.976 distance: 357 - 366: 17.517 distance: 358 - 359: 37.957 distance: 358 - 371: 40.427 distance: 360 - 361: 56.911 distance: 360 - 367: 23.487 distance: 361 - 362: 5.336 distance: 361 - 369: 23.223 distance: 361 - 370: 8.396 distance: 362 - 363: 17.165 distance: 362 - 364: 15.901 distance: 371 - 372: 42.688 distance: 371 - 377: 39.735 distance: 372 - 373: 13.661 distance: 372 - 375: 20.718 distance: 372 - 378: 24.110 distance: 373 - 374: 23.057 distance: 373 - 382: 36.832 distance: 375 - 376: 28.396 distance: 375 - 379: 15.038 distance: 375 - 380: 11.071 distance: 376 - 381: 27.668 distance: 382 - 383: 8.628 distance: 383 - 384: 5.116 distance: 383 - 386: 9.749 distance: 383 - 389: 10.448 distance: 384 - 385: 25.032 distance: 384 - 396: 30.428 distance: 386 - 391: 3.068 distance: 396 - 397: 13.126 distance: 396 - 400: 27.335 distance: 397 - 398: 16.106 distance: 397 - 401: 6.018 distance: 397 - 402: 37.877 distance: 398 - 399: 23.661 distance: 398 - 403: 43.268 distance: 403 - 404: 39.814 distance: 403 - 412: 39.952 distance: 404 - 405: 48.908 distance: 404 - 413: 40.254 distance: 405 - 406: 11.022 distance: 405 - 425: 29.435 distance: 407 - 408: 35.933 distance: 407 - 414: 21.557 distance: 407 - 415: 23.299 distance: 408 - 409: 3.257 distance: 408 - 416: 18.008 distance: 408 - 417: 8.808 distance: 409 - 410: 6.065 distance: 409 - 418: 5.404 distance: 409 - 419: 18.469 distance: 410 - 411: 11.350 distance: 411 - 422: 31.087 distance: 411 - 423: 8.621 distance: 411 - 424: 10.983 distance: 425 - 426: 26.561 distance: 425 - 432: 14.345 distance: 426 - 427: 24.743 distance: 426 - 429: 26.051 distance: 426 - 433: 15.545 distance: 427 - 428: 39.900 distance: 427 - 439: 38.866 distance: 429 - 430: 17.341 distance: 429 - 431: 44.040 distance: 429 - 434: 21.315 distance: 431 - 436: 21.494 distance: 431 - 438: 17.273 distance: 439 - 440: 65.266 distance: 439 - 447: 16.647 distance: 440 - 441: 30.515 distance: 440 - 443: 48.439 distance: 440 - 448: 64.499 distance: 441 - 442: 23.555 distance: 441 - 458: 52.381 distance: 443 - 444: 54.731 distance: 443 - 449: 54.340 distance: 443 - 450: 50.541 distance: 444 - 446: 23.030 distance: 445 - 452: 25.680 distance: 445 - 453: 3.638 distance: 445 - 454: 20.058 distance: 446 - 455: 14.249 distance: 446 - 456: 18.385 distance: 446 - 457: 22.823 distance: 458 - 459: 31.603 distance: 458 - 465: 27.459 distance: 459 - 460: 26.883 distance: 459 - 462: 39.954 distance: 459 - 466: 24.625 distance: 460 - 461: 11.703 distance: 460 - 472: 31.472 distance: 462 - 463: 32.208 distance: 462 - 464: 30.685 distance: 462 - 467: 45.928 distance: 463 - 468: 34.600 distance: 464 - 470: 30.442 distance: 464 - 471: 39.648