Starting phenix.real_space_refine on Fri Aug 2 18:58:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaq_26430/08_2024/7uaq_26430.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaq_26430/08_2024/7uaq_26430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaq_26430/08_2024/7uaq_26430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaq_26430/08_2024/7uaq_26430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaq_26430/08_2024/7uaq_26430.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uaq_26430/08_2024/7uaq_26430.cif" } resolution = 3.1 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= -0.003 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2773 2.51 5 N 723 2.21 5 O 850 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "H PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4362 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2392 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain breaks: 2 Chain: "H" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 997 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 833 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.61, per 1000 atoms: 0.83 Number of scatterers: 4362 At special positions: 0 Unit cell: (96.82, 64.89, 89.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 850 8.00 N 723 7.00 C 2773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " " NAG C 1 " - " ASN A 149 " " NAG D 1 " - " ASN A 234 " " NAG L 301 " - " ASN L 20 " Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 732.5 milliseconds 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 12 sheets defined 4.9% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.625A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 29 removed outlier: 3.625A pdb=" N ASN L 29 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.628A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.319A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.501A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.301A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA6, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.693A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 7 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 34 through 39 removed outlier: 7.162A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 88 through 89 removed outlier: 3.612A pdb=" N ALA H 88 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 93 through 95 removed outlier: 3.936A pdb=" N ILE H 112 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.524A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 44 through 50 removed outlier: 6.653A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER L 49 " --> pdb=" O ILE L 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) 91 hydrogen bonds defined for protein. 231 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: 1.01 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1293 1.34 - 1.46: 1224 1.46 - 1.59: 1933 1.59 - 1.72: 0 1.72 - 1.84: 22 Bond restraints: 4472 Sorted by residual: bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.02e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" N ILE A 197 " pdb=" CA ILE A 197 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.18e-02 7.18e+03 8.87e+00 bond pdb=" N ILE A 68 " pdb=" CA ILE A 68 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.85e+00 bond pdb=" N GLY L 101 " pdb=" CA GLY L 101 " ideal model delta sigma weight residual 1.447 1.474 -0.027 1.09e-02 8.42e+03 6.11e+00 ... (remaining 4467 not shown) Histogram of bond angle deviations from ideal: 97.22 - 104.62: 60 104.62 - 112.02: 2068 112.02 - 119.41: 1578 119.41 - 126.81: 2310 126.81 - 134.21: 57 Bond angle restraints: 6073 Sorted by residual: angle pdb=" C ASN A 165 " pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " ideal model delta sigma weight residual 110.42 122.89 -12.47 1.99e+00 2.53e-01 3.93e+01 angle pdb=" N ASN A 122 " pdb=" CA ASN A 122 " pdb=" CB ASN A 122 " ideal model delta sigma weight residual 110.45 101.66 8.79 1.44e+00 4.82e-01 3.73e+01 angle pdb=" CA GLY L 101 " pdb=" C GLY L 101 " pdb=" O GLY L 101 " ideal model delta sigma weight residual 122.29 117.98 4.31 8.10e-01 1.52e+00 2.83e+01 angle pdb=" N ASN A 165 " pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " ideal model delta sigma weight residual 110.49 101.68 8.81 1.69e+00 3.50e-01 2.72e+01 angle pdb=" N ASN L 20 " pdb=" CA ASN L 20 " pdb=" CB ASN L 20 " ideal model delta sigma weight residual 110.84 104.20 6.64 1.52e+00 4.33e-01 1.91e+01 ... (remaining 6068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.78: 2435 14.78 - 29.56: 219 29.56 - 44.34: 53 44.34 - 59.13: 28 59.13 - 73.91: 4 Dihedral angle restraints: 2739 sinusoidal: 1197 harmonic: 1542 Sorted by residual: dihedral pdb=" N ASN A 122 " pdb=" C ASN A 122 " pdb=" CA ASN A 122 " pdb=" CB ASN A 122 " ideal model delta harmonic sigma weight residual 122.80 110.48 12.32 0 2.50e+00 1.60e-01 2.43e+01 dihedral pdb=" CA GLN H 81 " pdb=" C GLN H 81 " pdb=" N MET H 82 " pdb=" CA MET H 82 " ideal model delta harmonic sigma weight residual -180.00 -156.77 -23.23 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA HIS L 54B" pdb=" C HIS L 54B" pdb=" N THR L 54C" pdb=" CA THR L 54C" ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 2736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 537 0.078 - 0.155: 128 0.155 - 0.233: 15 0.233 - 0.310: 3 0.310 - 0.388: 4 Chirality restraints: 687 Sorted by residual: chirality pdb=" C4 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C5 NAG C 1 " pdb=" O4 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.14 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 684 not shown) Planarity restraints: 773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " 0.010 2.00e-02 2.50e+03 7.50e-02 7.02e+01 pdb=" CG ASN A 165 " -0.093 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " -0.078 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 224 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.64e+01 pdb=" N PRO A 225 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO A 225 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 225 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " 0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" CG ASN A 165 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " 0.026 2.00e-02 2.50e+03 ... (remaining 770 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 125 2.66 - 3.22: 4192 3.22 - 3.78: 6567 3.78 - 4.34: 9038 4.34 - 4.90: 14761 Nonbonded interactions: 34683 Sorted by model distance: nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 102 " model vdw 2.101 3.040 nonbonded pdb=" OG1 THR L 22 " pdb=" OE2 GLU L 70 " model vdw 2.102 3.040 nonbonded pdb=" OE2 GLU A 96 " pdb=" N ASN A 99 " model vdw 2.158 3.120 nonbonded pdb=" O SER H 30 " pdb=" OG1 THR H 52A" model vdw 2.174 3.040 nonbonded pdb=" OE1 GLN A 14 " pdb=" NH1 ARG A 158 " model vdw 2.210 3.120 ... (remaining 34678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.690 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 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 : 0.006 0.061 4472 Z= 0.399 Angle : 1.187 12.470 6073 Z= 0.662 Chirality : 0.071 0.388 687 Planarity : 0.008 0.129 766 Dihedral : 13.129 73.906 1740 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 0.22 % Allowed : 0.86 % Favored : 98.92 % Cbeta Deviations : 0.41 % 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: -2.56 (0.35), residues: 523 helix: -0.03 (1.56), residues: 11 sheet: -0.76 (0.46), residues: 139 loop : -2.30 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 152 HIS 0.008 0.002 HIS H 106 PHE 0.032 0.003 PHE L 72 TYR 0.032 0.002 TYR A 144 ARG 0.007 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8280 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 158 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.8067 (mtt-85) REVERT: A 211 ASN cc_start: 0.8320 (p0) cc_final: 0.8032 (p0) REVERT: A 314 GLN cc_start: 0.6398 (tp40) cc_final: 0.6067 (tp40) REVERT: H 38 ARG cc_start: 0.6298 (ttm-80) cc_final: 0.6051 (ttm-80) REVERT: H 67 PHE cc_start: 0.7819 (m-80) cc_final: 0.7310 (m-80) REVERT: H 97 TYR cc_start: 0.7891 (t80) cc_final: 0.7566 (t80) REVERT: L 72 PHE cc_start: 0.7263 (m-10) cc_final: 0.6951 (m-80) outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.1589 time to fit residues: 26.5785 Evaluate side-chains 87 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4472 Z= 0.297 Angle : 0.868 11.774 6073 Z= 0.442 Chirality : 0.055 0.355 687 Planarity : 0.006 0.067 766 Dihedral : 8.570 57.436 794 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 3.02 % Allowed : 12.74 % Favored : 84.23 % 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: -2.41 (0.34), residues: 523 helix: 0.89 (1.65), residues: 11 sheet: -0.70 (0.43), residues: 145 loop : -2.23 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 35 HIS 0.006 0.002 HIS H 98 PHE 0.025 0.002 PHE A 238 TYR 0.026 0.002 TYR H 50 ARG 0.007 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7998 (tm-30) REVERT: A 190 ARG cc_start: 0.8210 (mtt-85) cc_final: 0.7787 (mtt-85) REVERT: A 298 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6363 (pt0) REVERT: A 314 GLN cc_start: 0.6485 (tp40) cc_final: 0.6096 (tp40) REVERT: H 107 SER cc_start: 0.7084 (p) cc_final: 0.6684 (p) REVERT: L 4 LEU cc_start: 0.7153 (pt) cc_final: 0.6864 (pt) REVERT: L 85 ASP cc_start: 0.7622 (m-30) cc_final: 0.6999 (m-30) outliers start: 14 outliers final: 8 residues processed: 107 average time/residue: 0.1712 time to fit residues: 23.0340 Evaluate side-chains 101 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 4472 Z= 0.464 Angle : 0.867 9.192 6073 Z= 0.446 Chirality : 0.053 0.329 687 Planarity : 0.006 0.055 766 Dihedral : 8.230 56.564 792 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.37 % Favored : 90.44 % Rotamer: Outliers : 4.54 % Allowed : 13.82 % Favored : 81.64 % 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: -2.32 (0.35), residues: 523 helix: 1.22 (1.80), residues: 11 sheet: -0.63 (0.43), residues: 152 loop : -2.20 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 91 HIS 0.007 0.002 HIS A 66 PHE 0.015 0.002 PHE A 238 TYR 0.024 0.002 TYR H 50 ARG 0.017 0.001 ARG L 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8311 (tm-30) cc_final: 0.8060 (tm-30) REVERT: A 132 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7343 (tm-30) REVERT: A 190 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7931 (mtt-85) REVERT: A 314 GLN cc_start: 0.6840 (tp40) cc_final: 0.6615 (tp40) REVERT: H 45 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8043 (pp) REVERT: H 57 ARG cc_start: 0.8396 (mmt-90) cc_final: 0.7858 (mmt-90) REVERT: H 107 SER cc_start: 0.7015 (p) cc_final: 0.6696 (p) REVERT: L 4 LEU cc_start: 0.7381 (pt) cc_final: 0.7130 (pt) REVERT: L 39 GLN cc_start: 0.8055 (tp-100) cc_final: 0.7771 (tm-30) REVERT: L 42 LYS cc_start: 0.8397 (mppt) cc_final: 0.7985 (mmtm) REVERT: L 45 ARG cc_start: 0.7649 (mtm110) cc_final: 0.7256 (ttp-110) REVERT: L 70 GLU cc_start: 0.8240 (pp20) cc_final: 0.7686 (pp20) REVERT: L 72 PHE cc_start: 0.7448 (m-80) cc_final: 0.6896 (t80) REVERT: L 85 ASP cc_start: 0.7877 (m-30) cc_final: 0.7610 (m-30) outliers start: 21 outliers final: 17 residues processed: 115 average time/residue: 0.1647 time to fit residues: 23.6193 Evaluate side-chains 113 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4472 Z= 0.245 Angle : 0.754 9.357 6073 Z= 0.382 Chirality : 0.051 0.322 687 Planarity : 0.005 0.049 766 Dihedral : 7.610 56.801 792 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.18 % Favored : 90.63 % Rotamer: Outliers : 5.40 % Allowed : 14.47 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.35), residues: 523 helix: 1.29 (1.82), residues: 11 sheet: -0.65 (0.43), residues: 145 loop : -2.14 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.006 0.002 HIS H 98 PHE 0.012 0.002 PHE A 318 TYR 0.021 0.002 TYR H 50 ARG 0.004 0.001 ARG L 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1046 Ramachandran restraints generated. 523 Oldfield, 0 Emsley, 523 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8036 (tm-30) REVERT: A 190 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7104 (mtp85) REVERT: A 298 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6360 (pt0) REVERT: H 45 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8002 (pp) REVERT: H 72 ASP cc_start: 0.7475 (p0) cc_final: 0.7063 (p0) REVERT: H 107 SER cc_start: 0.6977 (p) cc_final: 0.6759 (p) REVERT: L 4 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7064 (pt) REVERT: L 39 GLN cc_start: 0.7940 (tp-100) cc_final: 0.7686 (tm-30) REVERT: L 42 LYS cc_start: 0.8423 (mppt) cc_final: 0.7985 (mmtm) REVERT: L 45 ARG cc_start: 0.7567 (mtm110) cc_final: 0.7200 (ttp-110) REVERT: L 70 GLU cc_start: 0.8252 (pp20) cc_final: 0.7382 (pp20) REVERT: L 103 ARG cc_start: 0.8516 (mmm160) cc_final: 0.8235 (mmm160) outliers start: 25 outliers final: 14 residues processed: 117 average time/residue: 0.1673 time to fit residues: 24.4965 Evaluate side-chains 111 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 25 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/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-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/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-dev-5409/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-dev-5409/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: 51.7923 > 50: distance: 69 - 74: 10.020 distance: 74 - 75: 9.088 distance: 75 - 76: 15.619 distance: 75 - 78: 15.281 distance: 76 - 77: 9.227 distance: 76 - 82: 9.967 distance: 78 - 79: 12.406 distance: 79 - 80: 11.409 distance: 79 - 81: 10.379 distance: 82 - 83: 10.956 distance: 83 - 84: 13.460 distance: 83 - 86: 12.060 distance: 84 - 85: 20.779 distance: 84 - 91: 24.816 distance: 86 - 87: 16.573 distance: 87 - 88: 8.386 distance: 88 - 89: 13.856 distance: 89 - 90: 17.429 distance: 91 - 92: 7.810 distance: 92 - 93: 8.231 distance: 92 - 95: 20.581 distance: 93 - 94: 9.199 distance: 93 - 103: 8.762 distance: 95 - 96: 10.463 distance: 96 - 97: 5.729 distance: 96 - 98: 4.645 distance: 97 - 99: 9.030 distance: 98 - 100: 8.359 distance: 99 - 101: 5.012 distance: 100 - 101: 4.616 distance: 101 - 102: 20.080 distance: 103 - 104: 12.221 distance: 104 - 105: 18.115 distance: 104 - 107: 19.429 distance: 105 - 106: 16.252 distance: 105 - 111: 26.458 distance: 107 - 108: 16.778 distance: 108 - 109: 20.971 distance: 108 - 110: 14.005 distance: 111 - 112: 14.050 distance: 112 - 113: 10.260 distance: 112 - 115: 18.263 distance: 113 - 114: 11.772 distance: 113 - 120: 11.745 distance: 115 - 116: 17.306 distance: 116 - 117: 17.324 distance: 117 - 118: 28.059 distance: 117 - 119: 10.161 distance: 120 - 121: 10.538 distance: 121 - 122: 14.187 distance: 121 - 124: 11.568 distance: 122 - 123: 3.597 distance: 124 - 125: 17.201 distance: 125 - 126: 18.454 distance: 125 - 127: 17.605 distance: 127 - 172: 8.312 distance: 128 - 129: 6.571 distance: 129 - 130: 11.059 distance: 130 - 131: 15.128 distance: 132 - 133: 6.705 distance: 133 - 134: 6.337 distance: 133 - 136: 12.312 distance: 134 - 135: 8.875 distance: 134 - 139: 14.892 distance: 136 - 137: 15.089 distance: 136 - 138: 17.321 distance: 139 - 140: 15.726 distance: 140 - 141: 8.908 distance: 140 - 143: 8.416 distance: 141 - 142: 14.219 distance: 141 - 147: 12.138 distance: 143 - 144: 6.681 distance: 143 - 145: 15.578 distance: 144 - 146: 8.849 distance: 147 - 148: 5.362 distance: 148 - 149: 10.855 distance: 148 - 151: 9.530 distance: 149 - 150: 6.738 distance: 149 - 154: 10.361 distance: 151 - 152: 5.068 distance: 151 - 153: 9.059