Starting phenix.real_space_refine on Fri Aug 2 18:07:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9w_31499/08_2024/7f9w_31499.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9w_31499/08_2024/7f9w_31499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9w_31499/08_2024/7f9w_31499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9w_31499/08_2024/7f9w_31499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9w_31499/08_2024/7f9w_31499.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9w_31499/08_2024/7f9w_31499.cif" } resolution = 3.2 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= 0.023 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 22 5.16 5 C 2654 2.51 5 N 713 2.21 5 O 828 1.98 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-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4217 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 854 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 846 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 9, 'TRANS': 96} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 106, 846 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 9, 'TRANS': 96} Chain breaks: 2 bond proxies already assigned to first conformer: 863 Chain: "C" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1694 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "B" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1669 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 210} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AMET A 25 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 25 " occ=0.50 Time building chain proxies: 3.82, per 1000 atoms: 0.91 Number of scatterers: 4217 At special positions: 0 Unit cell: (64.26, 64.8, 116.1, 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 22 16.00 O 828 8.00 N 713 7.00 C 2654 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS B 205 " 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: 1.50 Conformation dependent library (CDL) restraints added in 926.6 milliseconds 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1016 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 15 sheets defined 5.9% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.834A pdb=" N VAL C 89 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 134 removed outlier: 3.700A pdb=" N LEU C 131 " --> pdb=" O SER C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 195 removed outlier: 3.727A pdb=" N LYS C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N HIS C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 210 through 213 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 3.705A pdb=" N GLN A 130 " --> pdb=" O THR A 14 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 145 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 21 removed outlier: 3.612A pdb=" N TYR A 20 " --> pdb=" O CYS A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 45 through 48 removed outlier: 3.878A pdb=" N LEU A 45 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.136A pdb=" N LEU C 11 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 90 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 91 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP C 41 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.532A pdb=" N THR C 78 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.811A pdb=" N LYS C 36 " --> pdb=" O TYR C 31 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.542A pdb=" N VAL C 139 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C 138 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 185 " --> pdb=" O VAL C 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 159 through 161 removed outlier: 4.827A pdb=" N TRP C 154 " --> pdb=" O GLN C 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 198 " --> pdb=" O PHE C 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.571A pdb=" N VAL B 18 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.459A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 33 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.459A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU B 111 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 129 through 133 removed outlier: 6.332A pdb=" N TYR B 185 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 129 through 133 removed outlier: 6.332A pdb=" N TYR B 185 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 162 through 163 142 hydrogen bonds defined for protein. 348 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: 1.07 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1349 1.34 - 1.46: 1038 1.46 - 1.58: 1904 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 4322 Sorted by residual: bond pdb=" CB PRO C 147 " pdb=" CG PRO C 147 " ideal model delta sigma weight residual 1.506 1.457 0.049 3.90e-02 6.57e+02 1.56e+00 bond pdb=" CB GLN C 96 " pdb=" CG GLN C 96 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.56e+00 bond pdb=" N ASN A 112 " pdb=" CA ASN A 112 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.26e+00 bond pdb=" C PHE C 104 " pdb=" N GLY C 105 " ideal model delta sigma weight residual 1.334 1.321 0.013 1.20e-02 6.94e+03 1.23e+00 bond pdb=" CB VAL C 29 " pdb=" CG1 VAL C 29 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.22e+00 ... (remaining 4317 not shown) Histogram of bond angle deviations from ideal: 96.99 - 104.41: 90 104.41 - 111.82: 2154 111.82 - 119.24: 1319 119.24 - 126.66: 2234 126.66 - 134.08: 78 Bond angle restraints: 5875 Sorted by residual: angle pdb=" C GLN C 96 " pdb=" N TYR C 97 " pdb=" CA TYR C 97 " ideal model delta sigma weight residual 122.65 116.83 5.82 1.66e+00 3.63e-01 1.23e+01 angle pdb=" N TYR C 146 " pdb=" CA TYR C 146 " pdb=" C TYR C 146 " ideal model delta sigma weight residual 108.82 103.55 5.27 1.69e+00 3.50e-01 9.74e+00 angle pdb=" C GLU A 111 " pdb=" N ASN A 112 " pdb=" CA ASN A 112 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.91e+00 angle pdb=" C HIS B 209 " pdb=" N LYS B 210 " pdb=" CA LYS B 210 " ideal model delta sigma weight residual 120.09 123.62 -3.53 1.25e+00 6.40e-01 7.99e+00 angle pdb=" C LEU B 133 " pdb=" N ALA B 134 " pdb=" CA ALA B 134 " ideal model delta sigma weight residual 120.60 124.34 -3.74 1.53e+00 4.27e-01 5.99e+00 ... (remaining 5870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 2385 16.30 - 32.61: 150 32.61 - 48.91: 40 48.91 - 65.21: 3 65.21 - 81.52: 13 Dihedral angle restraints: 2591 sinusoidal: 1004 harmonic: 1587 Sorted by residual: dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 94 " pdb=" CB CYS C 94 " ideal model delta sinusoidal sigma weight residual 93.00 159.24 -66.24 1 1.00e+01 1.00e-02 5.73e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 143.75 -50.75 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CA GLU A 113 " pdb=" C GLU A 113 " pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 2588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 348 0.027 - 0.054: 182 0.054 - 0.081: 59 0.081 - 0.107: 43 0.107 - 0.134: 14 Chirality restraints: 646 Sorted by residual: chirality pdb=" CA ILE C 54 " pdb=" N ILE C 54 " pdb=" C ILE C 54 " pdb=" CB ILE C 54 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA TYR C 97 " pdb=" N TYR C 97 " pdb=" C TYR C 97 " pdb=" CB TYR C 97 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL B 93 " pdb=" N VAL B 93 " pdb=" C VAL B 93 " pdb=" CB VAL B 93 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 643 not shown) Planarity restraints: 753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 56 " -0.015 2.00e-02 2.50e+03 1.72e-02 7.43e+00 pdb=" CG TRP C 56 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 56 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 56 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 56 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 56 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 56 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 56 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 56 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 56 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 134 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO B 135 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 135 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 135 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 155 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO B 156 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 156 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 156 " 0.021 5.00e-02 4.00e+02 ... (remaining 750 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 85 2.67 - 3.23: 3920 3.23 - 3.79: 6053 3.79 - 4.34: 8034 4.34 - 4.90: 13974 Nonbonded interactions: 32066 Sorted by model distance: nonbonded pdb=" OE2 GLU C 111 " pdb=" NE2 GLN C 172 " model vdw 2.114 3.120 nonbonded pdb=" OG SER B 212 " pdb=" OG1 THR B 214 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR A 47 " pdb=" O SER A 54 " model vdw 2.212 3.040 nonbonded pdb=" O SER C 83 " pdb=" NE2 GLN C 85 " model vdw 2.221 3.120 nonbonded pdb=" N GLY A 141 " pdb=" OG SER B 104 " model vdw 2.252 3.120 ... (remaining 32061 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.150 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.270 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 : 0.005 0.049 4322 Z= 0.334 Angle : 0.677 5.819 5875 Z= 0.371 Chirality : 0.043 0.134 646 Planarity : 0.005 0.053 753 Dihedral : 12.990 81.517 1557 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.63 % Allowed : 0.21 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.24 (0.38), residues: 539 helix: 0.20 (1.48), residues: 13 sheet: 0.41 (0.37), residues: 234 loop : 0.05 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 56 HIS 0.002 0.000 HIS B 173 PHE 0.014 0.002 PHE C 145 TYR 0.024 0.002 TYR C 97 ARG 0.004 0.001 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.472 Fit side-chains REVERT: A 18 MET cc_start: 0.8747 (mmp) cc_final: 0.8477 (mmt) REVERT: A 26 LEU cc_start: 0.6275 (tt) cc_final: 0.5996 (tt) REVERT: A 45 LEU cc_start: 0.8311 (tp) cc_final: 0.8091 (tt) REVERT: A 106 GLU cc_start: 0.8553 (pp20) cc_final: 0.8322 (pp20) REVERT: A 155 ARG cc_start: 0.8664 (ptm-80) cc_final: 0.8381 (tmt170) REVERT: A 160 GLN cc_start: 0.8279 (mm110) cc_final: 0.8026 (mm110) REVERT: C 1 ASP cc_start: 0.8395 (p0) cc_final: 0.8182 (p0) REVERT: C 128 ASP cc_start: 0.8519 (p0) cc_final: 0.8087 (p0) REVERT: C 153 GLN cc_start: 0.7248 (mp10) cc_final: 0.6837 (mp10) REVERT: B 59 ASP cc_start: 0.7667 (t0) cc_final: 0.7417 (t0) REVERT: B 73 ASP cc_start: 0.8333 (t0) cc_final: 0.8130 (t0) outliers start: 1 outliers final: 0 residues processed: 95 average time/residue: 0.1923 time to fit residues: 22.1783 Evaluate side-chains 83 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 GLN C 34 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN B 6 GLN B 65 GLN B 206 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4322 Z= 0.201 Angle : 0.628 6.566 5875 Z= 0.327 Chirality : 0.043 0.151 646 Planarity : 0.005 0.042 753 Dihedral : 4.703 22.128 589 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.63 % Allowed : 5.92 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.52 (0.39), residues: 539 helix: 0.80 (1.56), residues: 13 sheet: 0.53 (0.36), residues: 247 loop : 0.29 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 56 HIS 0.002 0.001 HIS A 103 PHE 0.016 0.001 PHE B 64 TYR 0.017 0.002 TYR C 97 ARG 0.005 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.471 Fit side-chains REVERT: A 9 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6968 (tm-30) REVERT: A 18 MET cc_start: 0.8719 (mmp) cc_final: 0.8459 (mmt) REVERT: A 126 MET cc_start: 0.8171 (ppp) cc_final: 0.7857 (ppp) REVERT: A 155 ARG cc_start: 0.8660 (ptm-80) cc_final: 0.8427 (tmt170) REVERT: A 160 GLN cc_start: 0.8293 (mm110) cc_final: 0.7923 (mm110) REVERT: C 1 ASP cc_start: 0.8342 (p0) cc_final: 0.8115 (p0) REVERT: C 17 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7647 (tm-30) REVERT: C 176 ASP cc_start: 0.8134 (m-30) cc_final: 0.7885 (t70) REVERT: B 59 ASP cc_start: 0.7602 (t0) cc_final: 0.7334 (t0) REVERT: B 64 PHE cc_start: 0.7491 (m-10) cc_final: 0.7262 (m-10) REVERT: B 73 ASP cc_start: 0.8352 (t0) cc_final: 0.8124 (t0) REVERT: B 100 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7908 (mtp-110) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1702 time to fit residues: 18.2821 Evaluate side-chains 80 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 8.9990 chunk 14 optimal weight: 0.0270 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.0370 chunk 52 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 47 optimal weight: 0.0050 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.6134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN C 34 ASN ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4322 Z= 0.166 Angle : 0.586 6.530 5875 Z= 0.305 Chirality : 0.042 0.158 646 Planarity : 0.004 0.034 753 Dihedral : 4.407 20.915 589 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.27 % Allowed : 9.73 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.59 (0.38), residues: 539 helix: 0.71 (1.56), residues: 13 sheet: 0.66 (0.35), residues: 244 loop : 0.27 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 156 HIS 0.002 0.000 HIS C 195 PHE 0.008 0.001 PHE B 64 TYR 0.013 0.001 TYR C 97 ARG 0.004 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.483 Fit side-chains REVERT: A 9 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7082 (tm-30) REVERT: A 18 MET cc_start: 0.8679 (mmp) cc_final: 0.8463 (mmt) REVERT: A 157 THR cc_start: 0.8293 (p) cc_final: 0.8036 (p) REVERT: A 160 GLN cc_start: 0.8279 (mm110) cc_final: 0.7922 (mm110) REVERT: C 1 ASP cc_start: 0.8284 (p0) cc_final: 0.8013 (p0) REVERT: C 17 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7766 (tm-30) REVERT: C 176 ASP cc_start: 0.8144 (m-30) cc_final: 0.7696 (t70) REVERT: B 59 ASP cc_start: 0.7639 (t0) cc_final: 0.7363 (t0) REVERT: B 73 ASP cc_start: 0.8371 (t0) cc_final: 0.8107 (t0) REVERT: B 100 ARG cc_start: 0.8169 (mtp-110) cc_final: 0.7854 (mtp-110) REVERT: B 116 THR cc_start: 0.8675 (m) cc_final: 0.8339 (p) REVERT: B 157 GLU cc_start: 0.8097 (pt0) cc_final: 0.7805 (pm20) REVERT: B 185 TYR cc_start: 0.8514 (m-80) cc_final: 0.8304 (m-80) outliers start: 4 outliers final: 2 residues processed: 90 average time/residue: 0.1554 time to fit residues: 17.7105 Evaluate side-chains 85 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 191 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 4322 Z= 0.378 Angle : 0.660 8.065 5875 Z= 0.347 Chirality : 0.045 0.166 646 Planarity : 0.005 0.039 753 Dihedral : 4.664 21.414 589 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.90 % Allowed : 11.63 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.45 (0.38), residues: 539 helix: 0.44 (1.49), residues: 13 sheet: 0.56 (0.36), residues: 242 loop : 0.18 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 41 HIS 0.002 0.000 HIS B 173 PHE 0.012 0.002 PHE B 64 TYR 0.033 0.002 TYR C 97 ARG 0.004 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.495 Fit side-chains REVERT: A 9 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7114 (tm-30) REVERT: A 18 MET cc_start: 0.8776 (mmp) cc_final: 0.8474 (mmt) REVERT: A 160 GLN cc_start: 0.8306 (mm110) cc_final: 0.7898 (mm110) REVERT: C 1 ASP cc_start: 0.8343 (p0) cc_final: 0.8074 (p0) REVERT: C 17 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7933 (tm-30) REVERT: B 59 ASP cc_start: 0.7702 (t0) cc_final: 0.7403 (t0) REVERT: B 73 ASP cc_start: 0.8390 (t0) cc_final: 0.8130 (t0) REVERT: B 157 GLU cc_start: 0.8146 (pt0) cc_final: 0.7894 (pm20) outliers start: 7 outliers final: 4 residues processed: 91 average time/residue: 0.1614 time to fit residues: 18.0965 Evaluate side-chains 87 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 43 optimal weight: 0.0170 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 1.2620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN C 96 GLN B 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4322 Z= 0.222 Angle : 0.604 7.930 5875 Z= 0.315 Chirality : 0.043 0.159 646 Planarity : 0.004 0.032 753 Dihedral : 4.533 21.211 589 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.33 % Allowed : 12.90 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.51 (0.38), residues: 539 helix: 0.58 (1.46), residues: 13 sheet: 0.72 (0.36), residues: 235 loop : 0.09 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 154 HIS 0.001 0.000 HIS B 173 PHE 0.016 0.001 PHE B 64 TYR 0.018 0.002 TYR C 97 ARG 0.006 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.510 Fit side-chains REVERT: A 9 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 18 MET cc_start: 0.8766 (mmp) cc_final: 0.8476 (mmt) REVERT: A 126 MET cc_start: 0.8175 (ppp) cc_final: 0.7861 (ppp) REVERT: A 144 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7071 (mt-10) REVERT: A 160 GLN cc_start: 0.8282 (mm110) cc_final: 0.7870 (mm110) REVERT: C 1 ASP cc_start: 0.8301 (p0) cc_final: 0.8043 (p0) REVERT: C 17 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7957 (tm-30) REVERT: C 176 ASP cc_start: 0.8091 (m-30) cc_final: 0.7881 (t70) REVERT: B 59 ASP cc_start: 0.7656 (t0) cc_final: 0.7374 (t0) REVERT: B 73 ASP cc_start: 0.8361 (t0) cc_final: 0.8098 (t0) REVERT: B 157 GLU cc_start: 0.8137 (pt0) cc_final: 0.7852 (pm20) outliers start: 9 outliers final: 4 residues processed: 92 average time/residue: 0.1778 time to fit residues: 20.1680 Evaluate side-chains 89 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain B residue 191 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 0.0030 chunk 51 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 0.0010 chunk 16 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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: 0.7733 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4322 Z= 0.156 Angle : 0.570 7.957 5875 Z= 0.296 Chirality : 0.042 0.149 646 Planarity : 0.004 0.037 753 Dihedral : 4.226 20.323 589 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.69 % Allowed : 13.11 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.65 (0.38), residues: 539 helix: 0.58 (1.42), residues: 13 sheet: 0.80 (0.35), residues: 237 loop : 0.20 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 154 HIS 0.002 0.000 HIS C 195 PHE 0.006 0.001 PHE A 121 TYR 0.013 0.001 TYR A 43 ARG 0.006 0.001 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7229 (tm-30) REVERT: A 18 MET cc_start: 0.8703 (mmp) cc_final: 0.8455 (mmt) REVERT: A 111 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8848 (mp0) REVERT: A 126 MET cc_start: 0.8165 (ppp) cc_final: 0.7873 (ppp) REVERT: A 144 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6976 (mt-10) REVERT: A 160 GLN cc_start: 0.8223 (mm110) cc_final: 0.7884 (mm110) REVERT: C 17 GLU cc_start: 0.8438 (tm-30) cc_final: 0.7949 (tm-30) REVERT: B 59 ASP cc_start: 0.7668 (t0) cc_final: 0.7388 (t0) REVERT: B 73 ASP cc_start: 0.8301 (t0) cc_final: 0.8044 (t0) REVERT: B 157 GLU cc_start: 0.8095 (pt0) cc_final: 0.7782 (pm20) REVERT: B 189 SER cc_start: 0.8832 (m) cc_final: 0.8356 (p) outliers start: 6 outliers final: 1 residues processed: 92 average time/residue: 0.1833 time to fit residues: 20.9017 Evaluate side-chains 81 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7757 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4322 Z= 0.186 Angle : 0.594 8.546 5875 Z= 0.308 Chirality : 0.042 0.150 646 Planarity : 0.004 0.037 753 Dihedral : 4.205 19.869 589 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.27 % Allowed : 14.59 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.56 (0.38), residues: 539 helix: 0.41 (1.42), residues: 13 sheet: 0.79 (0.36), residues: 235 loop : 0.12 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 156 HIS 0.001 0.000 HIS C 195 PHE 0.006 0.001 PHE C 215 TYR 0.013 0.001 TYR C 97 ARG 0.002 0.000 ARG C 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 9 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7278 (tm-30) REVERT: A 18 MET cc_start: 0.8729 (mmp) cc_final: 0.8452 (mmt) REVERT: A 111 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8831 (mp0) REVERT: A 126 MET cc_start: 0.8169 (ppp) cc_final: 0.7879 (ppp) REVERT: A 160 GLN cc_start: 0.8264 (mm110) cc_final: 0.7924 (mm110) REVERT: C 17 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7971 (tm-30) REVERT: B 59 ASP cc_start: 0.7681 (t0) cc_final: 0.7394 (t0) REVERT: B 73 ASP cc_start: 0.8313 (t0) cc_final: 0.8037 (t0) REVERT: B 157 GLU cc_start: 0.8064 (pt0) cc_final: 0.7782 (pm20) REVERT: B 189 SER cc_start: 0.8833 (m) cc_final: 0.8369 (p) outliers start: 4 outliers final: 1 residues processed: 87 average time/residue: 0.1740 time to fit residues: 18.8775 Evaluate side-chains 84 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 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: 0.7769 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4322 Z= 0.213 Angle : 0.600 8.777 5875 Z= 0.310 Chirality : 0.042 0.148 646 Planarity : 0.004 0.033 753 Dihedral : 4.224 18.911 589 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.48 % Allowed : 14.38 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.59 (0.38), residues: 539 helix: 0.51 (1.46), residues: 13 sheet: 0.82 (0.36), residues: 235 loop : 0.11 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 156 HIS 0.001 0.000 HIS B 173 PHE 0.006 0.001 PHE C 215 TYR 0.015 0.001 TYR C 97 ARG 0.004 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.492 Fit side-chains REVERT: A 9 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7289 (tm-30) REVERT: A 18 MET cc_start: 0.8749 (mmp) cc_final: 0.8447 (mmt) REVERT: A 126 MET cc_start: 0.8180 (ppp) cc_final: 0.7926 (ppp) REVERT: A 144 GLU cc_start: 0.7294 (mt-10) cc_final: 0.7032 (mt-10) REVERT: A 160 GLN cc_start: 0.8264 (mm110) cc_final: 0.7908 (mm110) REVERT: C 17 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8009 (tm-30) REVERT: C 111 GLU cc_start: 0.8077 (tp30) cc_final: 0.7755 (tt0) REVERT: B 59 ASP cc_start: 0.7703 (t0) cc_final: 0.7398 (t0) REVERT: B 73 ASP cc_start: 0.8304 (t0) cc_final: 0.8016 (t0) REVERT: B 157 GLU cc_start: 0.8062 (pt0) cc_final: 0.7772 (pm20) outliers start: 5 outliers final: 2 residues processed: 89 average time/residue: 0.1736 time to fit residues: 19.2470 Evaluate side-chains 84 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4322 Z= 0.329 Angle : 0.656 9.211 5875 Z= 0.342 Chirality : 0.044 0.150 646 Planarity : 0.004 0.033 753 Dihedral : 4.478 18.540 589 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.69 % Allowed : 15.01 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.51 (0.39), residues: 539 helix: 0.36 (1.40), residues: 13 sheet: 0.62 (0.36), residues: 243 loop : 0.21 (0.40), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 154 HIS 0.001 0.000 HIS B 173 PHE 0.008 0.001 PHE C 77 TYR 0.024 0.002 TYR C 97 ARG 0.003 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.663 Fit side-chains REVERT: A 9 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7216 (tm-30) REVERT: A 18 MET cc_start: 0.8799 (mmp) cc_final: 0.8460 (mmt) REVERT: A 160 GLN cc_start: 0.8300 (mm110) cc_final: 0.7933 (mm110) REVERT: C 17 GLU cc_start: 0.8488 (tm-30) cc_final: 0.7975 (tm-30) REVERT: C 111 GLU cc_start: 0.8104 (tp30) cc_final: 0.7784 (tt0) REVERT: C 129 GLU cc_start: 0.8705 (mp0) cc_final: 0.8421 (mp0) REVERT: C 176 ASP cc_start: 0.8275 (t70) cc_final: 0.7993 (t70) REVERT: B 59 ASP cc_start: 0.7732 (t0) cc_final: 0.7424 (t0) REVERT: B 73 ASP cc_start: 0.8319 (t0) cc_final: 0.8034 (t0) REVERT: B 157 GLU cc_start: 0.8071 (pt0) cc_final: 0.7790 (pm20) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 0.1755 time to fit residues: 19.3536 Evaluate side-chains 88 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 193 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 0.0980 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 6 optimal weight: 0.0050 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4322 Z= 0.173 Angle : 0.608 8.782 5875 Z= 0.309 Chirality : 0.042 0.146 646 Planarity : 0.004 0.030 753 Dihedral : 4.297 19.362 589 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.27 % Allowed : 15.86 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.62 % 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: 0.51 (0.38), residues: 539 helix: 0.53 (1.43), residues: 13 sheet: 0.71 (0.36), residues: 235 loop : 0.11 (0.39), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 156 HIS 0.001 0.000 HIS C 195 PHE 0.006 0.001 PHE A 121 TYR 0.011 0.001 TYR C 55 ARG 0.007 0.000 ARG A 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.516 Fit side-chains REVERT: A 9 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 18 MET cc_start: 0.8740 (mmp) cc_final: 0.8489 (mmt) REVERT: A 160 GLN cc_start: 0.8262 (mm110) cc_final: 0.7880 (mm110) REVERT: C 17 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7976 (tm-30) REVERT: C 111 GLU cc_start: 0.8062 (tp30) cc_final: 0.7753 (tt0) REVERT: C 129 GLU cc_start: 0.8694 (mp0) cc_final: 0.8445 (mp0) REVERT: B 59 ASP cc_start: 0.7707 (t0) cc_final: 0.7400 (t0) REVERT: B 73 ASP cc_start: 0.8307 (t0) cc_final: 0.8018 (t0) REVERT: B 157 GLU cc_start: 0.8038 (pt0) cc_final: 0.7716 (pm20) outliers start: 4 outliers final: 3 residues processed: 84 average time/residue: 0.1645 time to fit residues: 17.5181 Evaluate side-chains 85 residues out of total 471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 193 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 57.412 > 50: distance: 118 - 236: 28.049 distance: 121 - 233: 21.773 distance: 129 - 221: 31.075 distance: 132 - 218: 28.100 distance: 156 - 180: 25.394 distance: 172 - 177: 12.998 distance: 177 - 178: 9.471 distance: 178 - 179: 16.638 distance: 178 - 181: 7.783 distance: 179 - 180: 17.425 distance: 179 - 185: 28.721 distance: 181 - 182: 11.416 distance: 182 - 183: 25.000 distance: 182 - 184: 15.132 distance: 185 - 186: 36.854 distance: 186 - 187: 40.642 distance: 186 - 189: 57.412 distance: 187 - 188: 19.742 distance: 187 - 199: 11.552 distance: 189 - 190: 46.729 distance: 190 - 191: 31.451 distance: 190 - 192: 25.662 distance: 191 - 193: 10.829 distance: 192 - 194: 3.668 distance: 192 - 195: 6.565 distance: 193 - 194: 4.469 distance: 194 - 196: 6.078 distance: 195 - 197: 4.136 distance: 196 - 198: 5.469 distance: 197 - 198: 4.238 distance: 199 - 200: 36.781 distance: 200 - 201: 9.461 distance: 201 - 202: 30.046 distance: 201 - 203: 31.351 distance: 203 - 204: 10.585 distance: 204 - 205: 29.368 distance: 204 - 207: 28.602 distance: 205 - 206: 26.882 distance: 205 - 214: 30.961 distance: 207 - 208: 30.080 distance: 208 - 209: 19.456 distance: 209 - 210: 28.052 distance: 210 - 211: 11.304 distance: 211 - 212: 14.557 distance: 211 - 213: 18.743 distance: 214 - 215: 13.930 distance: 215 - 216: 55.303 distance: 216 - 217: 48.972 distance: 216 - 218: 46.300 distance: 218 - 219: 19.834 distance: 219 - 220: 17.770 distance: 219 - 222: 21.439 distance: 220 - 221: 39.355 distance: 220 - 225: 24.962 distance: 222 - 223: 36.797 distance: 222 - 224: 39.513 distance: 225 - 226: 33.046 distance: 226 - 227: 40.516 distance: 226 - 229: 9.437 distance: 227 - 228: 15.681 distance: 227 - 233: 14.247 distance: 229 - 230: 22.637 distance: 230 - 231: 46.491 distance: 230 - 232: 31.141 distance: 233 - 234: 13.751 distance: 234 - 235: 32.629 distance: 234 - 237: 29.860 distance: 235 - 236: 24.578 distance: 235 - 240: 27.257 distance: 237 - 238: 34.139 distance: 237 - 239: 37.371 distance: 240 - 241: 11.632 distance: 241 - 242: 15.688 distance: 241 - 244: 11.524 distance: 242 - 243: 12.262 distance: 242 - 247: 6.827 distance: 244 - 245: 20.125 distance: 244 - 246: 22.491 distance: 247 - 248: 12.532 distance: 248 - 249: 32.930 distance: 248 - 251: 11.975 distance: 249 - 250: 44.932 distance: 249 - 254: 28.991 distance: 251 - 252: 32.384 distance: 251 - 253: 31.832