Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 06:07:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0c_4692/04_2023/6r0c_4692.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0c_4692/04_2023/6r0c_4692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0c_4692/04_2023/6r0c_4692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0c_4692/04_2023/6r0c_4692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0c_4692/04_2023/6r0c_4692.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r0c_4692/04_2023/6r0c_4692.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.008 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 Mn 1 7.51 5 P 284 5.49 5 S 10 5.16 5 C 6504 2.51 5 N 2186 2.21 5 O 2752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 63": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11737 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "G" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 807 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2887 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "J" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2935 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.42, per 1000 atoms: 0.55 Number of scatterers: 11737 At special positions: 0 Unit cell: (118.81, 77.39, 117.72, 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) Mn 1 24.99 S 10 16.00 P 284 15.00 O 2752 8.00 N 2186 7.00 C 6504 6.00 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: 6.14 Conformation dependent library (CDL) restraints added in 1.2 seconds 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1390 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 74.6% alpha, 1.9% beta 137 base pairs and 246 stacking pairs defined. Time for finding SS restraints: 5.08 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.690A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.549A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.624A pdb=" N ILE A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.767A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.582A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.290A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 4.095A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.595A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.548A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.614A pdb=" N LEU C 115 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 116' Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.844A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.749A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.611A pdb=" N SER D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.614A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.580A pdb=" N ILE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.573A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.970A pdb=" N ARG F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 36 " --> pdb=" O PRO F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.233A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.744A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.812A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.752A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.545A pdb=" N LEU G 115 " --> pdb=" O GLN G 112 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 112 through 116' Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.843A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.748A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.612A pdb=" N SER H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.865A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.734A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.059A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.134A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.561A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 375 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 334 hydrogen bonds 652 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 246 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 6.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1985 1.33 - 1.45: 4170 1.45 - 1.56: 5783 1.56 - 1.68: 566 1.68 - 1.80: 18 Bond restraints: 12522 Sorted by residual: bond pdb=" C4' DT J -19 " pdb=" O4' DT J -19 " ideal model delta sigma weight residual 1.450 1.537 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C4' DC J -18 " pdb=" O4' DC J -18 " ideal model delta sigma weight residual 1.450 1.526 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C4' DC J -8 " pdb=" O4' DC J -8 " ideal model delta sigma weight residual 1.450 1.511 -0.061 2.00e-02 2.50e+03 9.34e+00 bond pdb=" C3' DT J 52 " pdb=" O3' DT J 52 " ideal model delta sigma weight residual 1.422 1.490 -0.068 3.00e-02 1.11e+03 5.08e+00 bond pdb=" C3' DA I 47 " pdb=" O3' DA I 47 " ideal model delta sigma weight residual 1.422 1.487 -0.065 3.00e-02 1.11e+03 4.73e+00 ... (remaining 12517 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.02: 1242 105.02 - 111.97: 6798 111.97 - 118.93: 3360 118.93 - 125.88: 5806 125.88 - 132.83: 925 Bond angle restraints: 18131 Sorted by residual: angle pdb=" C5' DC J -8 " pdb=" C4' DC J -8 " pdb=" O4' DC J -8 " ideal model delta sigma weight residual 109.40 102.57 6.83 1.50e+00 4.44e-01 2.07e+01 angle pdb=" C3' DA I 47 " pdb=" O3' DA I 47 " pdb=" P DG I 48 " ideal model delta sigma weight residual 120.20 126.04 -5.84 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C5' DT J -20 " pdb=" C4' DT J -20 " pdb=" O4' DT J -20 " ideal model delta sigma weight residual 109.40 103.88 5.52 1.50e+00 4.44e-01 1.35e+01 angle pdb=" C3' DT J 52 " pdb=" O3' DT J 52 " pdb=" P DC J 53 " ideal model delta sigma weight residual 120.20 125.72 -5.52 1.50e+00 4.44e-01 1.35e+01 angle pdb=" C4' DT J -19 " pdb=" O4' DT J -19 " pdb=" C1' DT J -19 " ideal model delta sigma weight residual 109.70 104.19 5.51 1.50e+00 4.44e-01 1.35e+01 ... (remaining 18126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 5218 35.81 - 71.63: 1306 71.63 - 107.44: 12 107.44 - 143.25: 0 143.25 - 179.07: 6 Dihedral angle restraints: 6542 sinusoidal: 4383 harmonic: 2159 Sorted by residual: dihedral pdb=" CA PHE A 84 " pdb=" C PHE A 84 " pdb=" N GLN A 85 " pdb=" CA GLN A 85 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ASN B 64 " pdb=" C ASN B 64 " pdb=" N VAL B 65 " pdb=" CA VAL B 65 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ILE B 50 " pdb=" C ILE B 50 " pdb=" N TYR B 51 " pdb=" CA TYR B 51 " ideal model delta harmonic sigma weight residual -180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 6539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1616 0.054 - 0.107: 379 0.107 - 0.161: 57 0.161 - 0.214: 9 0.214 - 0.268: 4 Chirality restraints: 2065 Sorted by residual: chirality pdb=" C4' DT J -19 " pdb=" C5' DT J -19 " pdb=" O4' DT J -19 " pdb=" C3' DT J -19 " both_signs ideal model delta sigma weight residual False -2.53 -2.79 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C4' DC J -8 " pdb=" C5' DC J -8 " pdb=" O4' DC J -8 " pdb=" C3' DC J -8 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C4' DC J -18 " pdb=" C5' DC J -18 " pdb=" O4' DC J -18 " pdb=" C3' DC J -18 " both_signs ideal model delta sigma weight residual False -2.53 -2.77 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 2062 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 63 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.52e+01 pdb=" C GLU B 63 " -0.067 2.00e-02 2.50e+03 pdb=" O GLU B 63 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN B 64 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 60 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.43e+00 pdb=" C VAL B 60 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL B 60 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE B 61 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 57 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C VAL B 57 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL B 57 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU B 58 " -0.015 2.00e-02 2.50e+03 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 33 2.50 - 3.10: 7576 3.10 - 3.70: 19941 3.70 - 4.30: 28089 4.30 - 4.90: 40773 Nonbonded interactions: 96412 Sorted by model distance: nonbonded pdb=" O2 DC I 42 " pdb=" N2 DG J -42 " model vdw 1.900 2.496 nonbonded pdb=" O2 DC I 37 " pdb=" N2 DG J -37 " model vdw 2.083 2.496 nonbonded pdb=" N3 DC I 42 " pdb=" N1 DG J -42 " model vdw 2.204 2.560 nonbonded pdb=" N3 DC I 37 " pdb=" N1 DG J -37 " model vdw 2.251 2.560 nonbonded pdb=" N2 DG I -2 " pdb=" O2 DC J 2 " model vdw 2.275 2.496 ... (remaining 96407 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 39 through 135) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 100) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.640 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: 0.010 Extract box with map and model: 4.480 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 37.760 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 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 : 0.008 0.087 12522 Z= 0.445 Angle : 0.865 8.749 18131 Z= 0.511 Chirality : 0.048 0.268 2065 Planarity : 0.007 0.051 1312 Dihedral : 27.846 179.067 5152 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.00 % 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: -2.35 (0.26), residues: 731 helix: -1.06 (0.18), residues: 523 sheet: None (None), residues: 0 loop : -2.54 (0.38), residues: 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.3632 time to fit residues: 145.0682 Evaluate side-chains 175 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 85 GLN H 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 12522 Z= 0.222 Angle : 0.648 11.967 18131 Z= 0.383 Chirality : 0.037 0.352 2065 Planarity : 0.005 0.038 1312 Dihedral : 32.221 179.757 3687 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.00 % 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: 0.28 (0.30), residues: 731 helix: 1.07 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -2.24 (0.39), residues: 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.3157 time to fit residues: 103.3293 Evaluate side-chains 182 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS E 68 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 12522 Z= 0.310 Angle : 0.665 11.279 18131 Z= 0.390 Chirality : 0.037 0.283 2065 Planarity : 0.004 0.039 1312 Dihedral : 32.061 178.794 3687 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.31), residues: 731 helix: 1.80 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -2.50 (0.38), residues: 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.2958 time to fit residues: 86.0915 Evaluate side-chains 170 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 12522 Z= 0.309 Angle : 0.654 11.040 18131 Z= 0.383 Chirality : 0.037 0.248 2065 Planarity : 0.004 0.041 1312 Dihedral : 31.979 177.870 3687 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.00 % 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: 1.46 (0.31), residues: 731 helix: 2.07 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -2.24 (0.39), residues: 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2800 time to fit residues: 77.4034 Evaluate side-chains 167 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.885 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 71 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 12522 Z= 0.192 Angle : 0.596 5.366 18131 Z= 0.356 Chirality : 0.034 0.131 2065 Planarity : 0.004 0.043 1312 Dihedral : 31.853 178.501 3687 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.31), residues: 731 helix: 2.31 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -2.09 (0.39), residues: 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.2533 time to fit residues: 74.4988 Evaluate side-chains 174 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 12522 Z= 0.186 Angle : 0.589 5.916 18131 Z= 0.351 Chirality : 0.034 0.139 2065 Planarity : 0.003 0.041 1312 Dihedral : 31.744 177.950 3687 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.00 % 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: 1.93 (0.31), residues: 731 helix: 2.39 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -2.07 (0.39), residues: 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2592 time to fit residues: 74.4771 Evaluate side-chains 167 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1048 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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-1.21rc1-4938/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: 50.7692 > 50: distance: 23 - 25: 6.223 distance: 25 - 26: 20.813 distance: 26 - 27: 18.752 distance: 26 - 29: 24.923 distance: 27 - 28: 21.066 distance: 27 - 33: 22.090 distance: 29 - 30: 15.981 distance: 30 - 31: 23.284 distance: 30 - 32: 34.083 distance: 33 - 34: 9.897 distance: 34 - 35: 10.400 distance: 34 - 37: 3.762 distance: 35 - 42: 9.851 distance: 37 - 38: 16.339 distance: 38 - 39: 9.290 distance: 39 - 40: 18.636 distance: 39 - 41: 14.597 distance: 42 - 43: 8.493 distance: 43 - 44: 10.416 distance: 43 - 46: 4.040 distance: 44 - 45: 11.806 distance: 44 - 53: 7.532 distance: 46 - 47: 7.453 distance: 47 - 48: 3.868 distance: 48 - 50: 10.110 distance: 49 - 51: 6.784 distance: 50 - 52: 3.386 distance: 51 - 52: 5.731 distance: 53 - 54: 10.650 distance: 53 - 59: 13.351 distance: 54 - 55: 12.329 distance: 54 - 57: 6.911 distance: 55 - 56: 10.020 distance: 55 - 60: 3.292 distance: 56 - 82: 15.593 distance: 57 - 58: 11.192 distance: 58 - 59: 17.032 distance: 60 - 61: 3.261 distance: 61 - 62: 3.614 distance: 61 - 64: 5.457 distance: 62 - 67: 4.043 distance: 63 - 89: 8.435 distance: 64 - 65: 7.359 distance: 64 - 66: 14.089 distance: 67 - 68: 4.928 distance: 68 - 69: 8.186 distance: 69 - 70: 10.482 distance: 69 - 71: 4.486 distance: 70 - 99: 11.747 distance: 71 - 72: 8.771 distance: 72 - 73: 5.149 distance: 72 - 75: 13.495 distance: 73 - 74: 5.700 distance: 74 - 110: 14.455 distance: 75 - 76: 7.135 distance: 76 - 77: 15.082 distance: 77 - 78: 4.070 distance: 78 - 79: 11.667 distance: 79 - 80: 4.418 distance: 79 - 81: 6.215 distance: 82 - 83: 3.216 distance: 83 - 84: 4.885 distance: 84 - 85: 5.264 distance: 84 - 89: 3.190 distance: 85 - 118: 14.827 distance: 86 - 87: 8.807 distance: 86 - 88: 8.780 distance: 89 - 90: 5.048 distance: 90 - 91: 4.312 distance: 90 - 93: 4.428 distance: 91 - 99: 5.362 distance: 92 - 125: 11.641 distance: 94 - 95: 7.392 distance: 94 - 96: 7.688 distance: 95 - 97: 5.500 distance: 96 - 98: 6.310 distance: 97 - 98: 8.587 distance: 99 - 100: 6.651 distance: 100 - 101: 5.414 distance: 100 - 103: 3.065 distance: 101 - 102: 6.234 distance: 101 - 110: 3.639 distance: 102 - 135: 7.473 distance: 103 - 104: 8.899 distance: 104 - 105: 5.706 distance: 105 - 106: 7.642 distance: 106 - 107: 11.766 distance: 107 - 108: 12.903 distance: 107 - 109: 8.860