Starting phenix.real_space_refine on Sat Mar 9 15:46:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/03_2024/5lii_4053.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/03_2024/5lii_4053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/03_2024/5lii_4053.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/03_2024/5lii_4053.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/03_2024/5lii_4053.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5lii_4053/03_2024/5lii_4053.pdb" } resolution = 3.8 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= 0.270 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 11 5.16 5 C 1947 2.51 5 N 545 2.21 5 O 595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3098 Number of models: 1 Model: "" Number of chains: 1 Chain: "P" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3098 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 414} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 350 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 3, 'ASN:plan1': 7, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 154 Time building chain proxies: 1.36, per 1000 atoms: 0.44 Number of scatterers: 3098 At special positions: 0 Unit cell: (66.24, 100.74, 97.98, 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 11 16.00 O 595 8.00 N 545 7.00 C 1947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 365.7 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 806 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 5 sheets defined 11.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'P' and resid 63 through 68 Processing helix chain 'P' and resid 125 through 131 Processing helix chain 'P' and resid 137 through 159 removed outlier: 3.620A pdb=" N THR P 142 " --> pdb=" O SER P 138 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU P 154 " --> pdb=" O ALA P 150 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR P 159 " --> pdb=" O TRP P 155 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 210 removed outlier: 3.528A pdb=" N ASN P 201 " --> pdb=" O GLU P 197 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY P 210 " --> pdb=" O ARG P 206 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 70 through 72 removed outlier: 6.829A pdb=" N ARG P 71 " --> pdb=" O GLU P 418 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 82 through 84 Processing sheet with id=AA3, first strand: chain 'P' and resid 325 through 326 removed outlier: 3.509A pdb=" N SER P 326 " --> pdb=" O ILE P 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'P' and resid 348 through 350 Processing sheet with id=AA5, first strand: chain 'P' and resid 404 through 407 41 hydrogen bonds defined for protein. 114 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: 0.40 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 542 1.27 - 1.41: 749 1.41 - 1.55: 1832 1.55 - 1.69: 3 1.69 - 1.83: 22 Bond restraints: 3148 Sorted by residual: bond pdb=" C ALA P 101 " pdb=" N PRO P 102 " ideal model delta sigma weight residual 1.334 1.134 0.200 2.34e-02 1.83e+03 7.32e+01 bond pdb=" CA MET P 409 " pdb=" CB MET P 409 " ideal model delta sigma weight residual 1.528 1.420 0.109 1.35e-02 5.49e+03 6.47e+01 bond pdb=" CB TYR P 441 " pdb=" CG TYR P 441 " ideal model delta sigma weight residual 1.512 1.445 0.067 2.20e-02 2.07e+03 9.31e+00 bond pdb=" CG LEU P 181 " pdb=" CD1 LEU P 181 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.04e+00 bond pdb=" CB PRO P 137 " pdb=" CG PRO P 137 " ideal model delta sigma weight residual 1.506 1.400 0.106 3.90e-02 6.57e+02 7.41e+00 ... (remaining 3143 not shown) Histogram of bond angle deviations from ideal: 65.95 - 85.26: 4 85.26 - 104.56: 78 104.56 - 123.86: 4090 123.86 - 143.16: 112 143.16 - 162.47: 2 Bond angle restraints: 4286 Sorted by residual: angle pdb=" N PRO P 399 " pdb=" CA PRO P 399 " pdb=" CB PRO P 399 " ideal model delta sigma weight residual 102.60 65.95 36.65 1.10e+00 8.26e-01 1.11e+03 angle pdb=" N VAL P 118 " pdb=" CA VAL P 118 " pdb=" CB VAL P 118 " ideal model delta sigma weight residual 110.49 78.16 32.33 1.15e+00 7.56e-01 7.90e+02 angle pdb=" N LEU P 398 " pdb=" CA LEU P 398 " pdb=" C LEU P 398 " ideal model delta sigma weight residual 107.91 149.33 -41.42 2.05e+00 2.38e-01 4.08e+02 angle pdb=" N PRO P 399 " pdb=" CD PRO P 399 " pdb=" CG PRO P 399 " ideal model delta sigma weight residual 103.80 79.83 23.97 1.20e+00 6.94e-01 3.99e+02 angle pdb=" N PRO P 399 " pdb=" CA PRO P 399 " pdb=" C PRO P 399 " ideal model delta sigma weight residual 112.10 162.47 -50.37 2.60e+00 1.48e-01 3.75e+02 ... (remaining 4281 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 10.87: 1509 10.87 - 21.73: 277 21.73 - 32.60: 73 32.60 - 43.46: 16 43.46 - 54.32: 6 Dihedral angle restraints: 1881 sinusoidal: 631 harmonic: 1250 Sorted by residual: dihedral pdb=" N VAL P 118 " pdb=" C VAL P 118 " pdb=" CA VAL P 118 " pdb=" CB VAL P 118 " ideal model delta harmonic sigma weight residual 123.40 88.32 35.08 0 2.50e+00 1.60e-01 1.97e+02 dihedral pdb=" CA LYS P 394 " pdb=" C LYS P 394 " pdb=" N ASN P 395 " pdb=" CA ASN P 395 " ideal model delta harmonic sigma weight residual 180.00 -129.42 -50.58 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" N LEU P 398 " pdb=" C LEU P 398 " pdb=" CA LEU P 398 " pdb=" CB LEU P 398 " ideal model delta harmonic sigma weight residual 122.80 144.26 -21.46 0 2.50e+00 1.60e-01 7.37e+01 ... (remaining 1878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.366: 500 0.366 - 0.732: 1 0.732 - 1.098: 1 1.098 - 1.464: 0 1.464 - 1.829: 2 Chirality restraints: 504 Sorted by residual: chirality pdb=" CA PRO P 399 " pdb=" N PRO P 399 " pdb=" C PRO P 399 " pdb=" CB PRO P 399 " both_signs ideal model delta sigma weight residual False 2.72 0.89 1.83 2.00e-01 2.50e+01 8.37e+01 chirality pdb=" CA LEU P 398 " pdb=" N LEU P 398 " pdb=" C LEU P 398 " pdb=" CB LEU P 398 " both_signs ideal model delta sigma weight residual False 2.51 0.99 1.52 2.00e-01 2.50e+01 5.79e+01 chirality pdb=" CA ASN P 133 " pdb=" N ASN P 133 " pdb=" C ASN P 133 " pdb=" CB ASN P 133 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 501 not shown) Planarity restraints: 564 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU P 398 " 0.143 5.00e-02 4.00e+02 2.09e-01 7.02e+01 pdb=" N PRO P 399 " -0.359 5.00e-02 4.00e+02 pdb=" CA PRO P 399 " 0.147 5.00e-02 4.00e+02 pdb=" CD PRO P 399 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 261 " 0.029 2.00e-02 2.50e+03 2.01e-02 7.10e+00 pdb=" CG PHE P 261 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE P 261 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE P 261 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE P 261 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE P 261 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE P 261 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR P 256 " 0.023 2.00e-02 2.50e+03 1.86e-02 6.89e+00 pdb=" CG TYR P 256 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR P 256 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR P 256 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR P 256 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR P 256 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR P 256 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR P 256 " -0.001 2.00e-02 2.50e+03 ... (remaining 561 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 45 2.46 - 3.07: 2532 3.07 - 3.68: 4232 3.68 - 4.29: 5645 4.29 - 4.90: 8788 Nonbonded interactions: 21242 Sorted by model distance: nonbonded pdb=" O ASN P 229 " pdb=" OD1 ASN P 229 " model vdw 1.855 3.040 nonbonded pdb=" CE2 TYR P 117 " pdb=" CG2 THR P 152 " model vdw 1.987 3.760 nonbonded pdb=" O LEU P 398 " pdb=" CD PRO P 399 " model vdw 2.081 2.752 nonbonded pdb=" O GLY P 233 " pdb=" NH1 ARG P 234 " model vdw 2.082 2.520 nonbonded pdb=" OG SER P 75 " pdb=" O VAL P 78 " model vdw 2.093 2.440 ... (remaining 21237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 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: 0.450 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.550 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:2.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 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 : 0.015 0.200 3148 Z= 0.963 Angle : 2.407 50.367 4286 Z= 1.473 Chirality : 0.139 1.829 504 Planarity : 0.012 0.209 564 Dihedral : 12.691 54.322 1075 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 42.83 Ramachandran Plot: Outliers : 1.16 % Allowed : 16.94 % Favored : 81.90 % Rotamer: Outliers : 1.41 % Allowed : 6.01 % Favored : 92.58 % Cbeta Deviations : 1.49 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 16.67 % Twisted General : 1.93 % 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: -6.10 (0.25), residues: 431 helix: -4.70 (0.36), residues: 55 sheet: -1.38 (0.90), residues: 28 loop : -4.65 (0.20), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP P 440 HIS 0.011 0.005 HIS P 86 PHE 0.044 0.006 PHE P 94 TYR 0.046 0.005 TYR P 256 ARG 0.010 0.002 ARG P 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 37 GLN cc_start: 0.8674 (pm20) cc_final: 0.8415 (pm20) REVERT: P 65 TYR cc_start: 0.8667 (t80) cc_final: 0.8349 (t80) REVERT: P 109 ARG cc_start: 0.7061 (mtp180) cc_final: 0.6511 (mtt90) REVERT: P 133 ASN cc_start: 0.7821 (m-40) cc_final: 0.7415 (m-40) REVERT: P 184 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7947 (mtpt) REVERT: P 268 THR cc_start: 0.8176 (p) cc_final: 0.7792 (p) REVERT: P 393 ASP cc_start: 0.7378 (m-30) cc_final: 0.7103 (m-30) REVERT: P 424 LYS cc_start: 0.8253 (ptmt) cc_final: 0.8004 (ptmt) outliers start: 4 outliers final: 2 residues processed: 84 average time/residue: 0.0929 time to fit residues: 9.4751 Evaluate side-chains 59 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 207 ILE Chi-restraints excluded: chain P residue 399 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 229 ASN ** P 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3148 Z= 0.209 Angle : 0.896 10.261 4286 Z= 0.475 Chirality : 0.049 0.190 504 Planarity : 0.006 0.074 564 Dihedral : 9.352 33.239 464 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.46 % Favored : 85.85 % Rotamer: Outliers : 5.30 % Allowed : 12.01 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -5.34 (0.30), residues: 431 helix: -2.61 (0.63), residues: 54 sheet: -0.87 (1.24), residues: 23 loop : -4.35 (0.23), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 452 HIS 0.003 0.001 HIS P 265 PHE 0.018 0.002 PHE P 373 TYR 0.022 0.003 TYR P 441 ARG 0.002 0.001 ARG P 459 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: P 37 GLN cc_start: 0.8670 (pm20) cc_final: 0.8258 (pm20) REVERT: P 154 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6291 (pm20) REVERT: P 184 LYS cc_start: 0.7500 (mtmm) cc_final: 0.7272 (mtpt) REVERT: P 219 MET cc_start: 0.6621 (tpp) cc_final: 0.6167 (mmt) REVERT: P 268 THR cc_start: 0.7903 (p) cc_final: 0.7389 (p) REVERT: P 431 ASN cc_start: 0.8052 (m-40) cc_final: 0.7680 (m-40) outliers start: 15 outliers final: 6 residues processed: 79 average time/residue: 0.1013 time to fit residues: 9.5906 Evaluate side-chains 62 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 148 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 433 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3148 Z= 0.277 Angle : 0.893 11.840 4286 Z= 0.471 Chirality : 0.050 0.186 504 Planarity : 0.007 0.101 564 Dihedral : 8.677 27.593 459 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.70 % Allowed : 17.87 % Favored : 81.44 % Rotamer: Outliers : 6.71 % Allowed : 16.61 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % 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: -5.27 (0.31), residues: 431 helix: -2.51 (0.63), residues: 61 sheet: -0.59 (1.14), residues: 28 loop : -4.39 (0.24), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP P 452 HIS 0.006 0.002 HIS P 415 PHE 0.020 0.003 PHE P 261 TYR 0.022 0.003 TYR P 83 ARG 0.004 0.000 ARG P 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 0.206 Fit side-chains REVERT: P 71 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7471 (ttm110) REVERT: P 93 ARG cc_start: 0.7752 (tpp80) cc_final: 0.7445 (tpp80) REVERT: P 154 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6574 (pm20) REVERT: P 198 LYS cc_start: 0.8355 (ttpp) cc_final: 0.6633 (tppt) REVERT: P 263 LYS cc_start: 0.7747 (pttm) cc_final: 0.7533 (ptpp) REVERT: P 265 HIS cc_start: 0.6786 (t-90) cc_final: 0.6473 (t-170) REVERT: P 431 ASN cc_start: 0.8484 (m-40) cc_final: 0.8100 (m-40) outliers start: 19 outliers final: 12 residues processed: 78 average time/residue: 0.1082 time to fit residues: 10.0198 Evaluate side-chains 70 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 181 LEU Chi-restraints excluded: chain P residue 183 ASP Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 433 SER Chi-restraints excluded: chain P residue 454 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 20 optimal weight: 0.0570 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 384 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3148 Z= 0.180 Angle : 0.794 12.538 4286 Z= 0.409 Chirality : 0.045 0.148 504 Planarity : 0.006 0.089 564 Dihedral : 7.660 28.498 459 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.46 % Favored : 85.85 % Rotamer: Outliers : 7.77 % Allowed : 18.37 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.32), residues: 431 helix: -1.98 (0.67), residues: 54 sheet: -0.47 (1.14), residues: 28 loop : -4.16 (0.25), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP P 57 HIS 0.002 0.001 HIS P 91 PHE 0.013 0.002 PHE P 373 TYR 0.018 0.002 TYR P 441 ARG 0.002 0.000 ARG P 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 0.205 Fit side-chains REVERT: P 37 GLN cc_start: 0.8647 (pm20) cc_final: 0.8184 (pm20) REVERT: P 51 GLN cc_start: 0.8088 (mm110) cc_final: 0.7875 (mm-40) REVERT: P 71 ARG cc_start: 0.7757 (mtm110) cc_final: 0.7134 (ttm110) REVERT: P 93 ARG cc_start: 0.7752 (tpp80) cc_final: 0.7474 (tpp80) REVERT: P 109 ARG cc_start: 0.5319 (mpt180) cc_final: 0.4985 (mtt90) REVERT: P 154 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6259 (pm20) REVERT: P 173 LEU cc_start: 0.7323 (tp) cc_final: 0.7033 (tt) REVERT: P 263 LYS cc_start: 0.7794 (pttm) cc_final: 0.7419 (ptmm) REVERT: P 389 ILE cc_start: 0.6907 (mp) cc_final: 0.6551 (pt) REVERT: P 395 ASN cc_start: 0.4851 (t0) cc_final: 0.3660 (p0) REVERT: P 459 ARG cc_start: 0.6601 (mtp-110) cc_final: 0.6270 (ttp-170) outliers start: 22 outliers final: 15 residues processed: 85 average time/residue: 0.1056 time to fit residues: 10.6637 Evaluate side-chains 74 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 58 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 161 ASP Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 433 SER Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 0.0770 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3148 Z= 0.284 Angle : 0.860 12.593 4286 Z= 0.453 Chirality : 0.048 0.172 504 Planarity : 0.007 0.090 564 Dihedral : 7.968 26.130 459 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.70 % Allowed : 17.87 % Favored : 81.44 % Rotamer: Outliers : 8.83 % Allowed : 18.73 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.33), residues: 431 helix: -2.38 (0.61), residues: 61 sheet: -0.19 (1.21), residues: 28 loop : -4.17 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP P 57 HIS 0.003 0.001 HIS P 91 PHE 0.022 0.003 PHE P 261 TYR 0.025 0.003 TYR P 441 ARG 0.003 0.000 ARG P 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 64 time to evaluate : 0.206 Fit side-chains REVERT: P 37 GLN cc_start: 0.8575 (pm20) cc_final: 0.8052 (pm20) REVERT: P 71 ARG cc_start: 0.7898 (mtm110) cc_final: 0.7292 (ttm110) REVERT: P 154 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6325 (pm20) REVERT: P 173 LEU cc_start: 0.7480 (tp) cc_final: 0.7263 (tt) REVERT: P 198 LYS cc_start: 0.8453 (ttpp) cc_final: 0.6749 (tppt) REVERT: P 263 LYS cc_start: 0.7769 (pttm) cc_final: 0.7554 (ptmm) REVERT: P 458 VAL cc_start: 0.6600 (OUTLIER) cc_final: 0.6400 (t) REVERT: P 460 TYR cc_start: 0.3151 (OUTLIER) cc_final: 0.0819 (p90) outliers start: 25 outliers final: 19 residues processed: 81 average time/residue: 0.1077 time to fit residues: 10.3636 Evaluate side-chains 84 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 161 ASP Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 433 SER Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Chi-restraints excluded: chain P residue 460 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 40 optimal weight: 0.0000 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3148 Z= 0.181 Angle : 0.767 13.095 4286 Z= 0.396 Chirality : 0.044 0.143 504 Planarity : 0.006 0.082 564 Dihedral : 7.299 26.893 459 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.46 % Favored : 85.85 % Rotamer: Outliers : 7.77 % Allowed : 19.79 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.73 (0.33), residues: 431 helix: -2.18 (0.62), residues: 61 sheet: -0.16 (1.18), residues: 28 loop : -3.99 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP P 57 HIS 0.001 0.001 HIS P 415 PHE 0.014 0.002 PHE P 373 TYR 0.015 0.002 TYR P 441 ARG 0.002 0.000 ARG P 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 0.206 Fit side-chains REVERT: P 30 TYR cc_start: 0.3424 (OUTLIER) cc_final: 0.2895 (m-80) REVERT: P 37 GLN cc_start: 0.8621 (pm20) cc_final: 0.8147 (pm20) REVERT: P 71 ARG cc_start: 0.7668 (mtm110) cc_final: 0.7190 (ttm110) REVERT: P 154 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6313 (pm20) REVERT: P 198 LYS cc_start: 0.8424 (ttpp) cc_final: 0.6699 (tppt) REVERT: P 263 LYS cc_start: 0.7717 (pttm) cc_final: 0.7370 (ptmm) REVERT: P 265 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.6215 (t-90) REVERT: P 371 MET cc_start: 0.5850 (mtt) cc_final: 0.5525 (mmm) REVERT: P 377 ARG cc_start: 0.6640 (mmt90) cc_final: 0.6390 (mmt90) REVERT: P 395 ASN cc_start: 0.4935 (t0) cc_final: 0.3754 (p0) REVERT: P 458 VAL cc_start: 0.6554 (OUTLIER) cc_final: 0.6294 (t) REVERT: P 459 ARG cc_start: 0.6839 (mtp-110) cc_final: 0.6470 (ttp-170) outliers start: 22 outliers final: 17 residues processed: 83 average time/residue: 0.1136 time to fit residues: 11.0998 Evaluate side-chains 79 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 58 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 161 ASP Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 265 HIS Chi-restraints excluded: chain P residue 373 PHE Chi-restraints excluded: chain P residue 433 SER Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.0030 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 26 optimal weight: 9.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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: 0.6571 moved from start: 0.5389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3148 Z= 0.168 Angle : 0.728 13.031 4286 Z= 0.374 Chirality : 0.043 0.141 504 Planarity : 0.006 0.081 564 Dihedral : 6.750 26.007 459 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.55 % Favored : 83.76 % Rotamer: Outliers : 9.54 % Allowed : 19.43 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.33), residues: 431 helix: -1.98 (0.61), residues: 61 sheet: -0.37 (1.09), residues: 28 loop : -3.88 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 57 HIS 0.002 0.001 HIS P 415 PHE 0.011 0.001 PHE P 373 TYR 0.017 0.002 TYR P 218 ARG 0.002 0.000 ARG P 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 62 time to evaluate : 0.205 Fit side-chains REVERT: P 30 TYR cc_start: 0.3620 (OUTLIER) cc_final: 0.2999 (m-80) REVERT: P 37 GLN cc_start: 0.8591 (pm20) cc_final: 0.8106 (pm20) REVERT: P 71 ARG cc_start: 0.7812 (mtm110) cc_final: 0.7423 (ttm110) REVERT: P 154 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6282 (pm20) REVERT: P 198 LYS cc_start: 0.8380 (ttpp) cc_final: 0.6771 (tppt) REVERT: P 263 LYS cc_start: 0.7717 (pttm) cc_final: 0.7515 (ptmm) REVERT: P 265 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.6368 (t-90) REVERT: P 377 ARG cc_start: 0.6330 (mmt90) cc_final: 0.6093 (mmt90) REVERT: P 395 ASN cc_start: 0.4662 (t0) cc_final: 0.3809 (p0) REVERT: P 431 ASN cc_start: 0.7938 (m110) cc_final: 0.7208 (t0) REVERT: P 454 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7052 (ptm-80) REVERT: P 458 VAL cc_start: 0.6431 (OUTLIER) cc_final: 0.6216 (t) outliers start: 27 outliers final: 18 residues processed: 83 average time/residue: 0.1001 time to fit residues: 9.9854 Evaluate side-chains 81 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 58 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 161 ASP Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 205 VAL Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 265 HIS Chi-restraints excluded: chain P residue 433 SER Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.0570 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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: 0.6550 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3148 Z= 0.167 Angle : 0.724 13.253 4286 Z= 0.370 Chirality : 0.043 0.141 504 Planarity : 0.006 0.082 564 Dihedral : 6.486 24.541 459 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.70 % Allowed : 13.92 % Favored : 85.38 % Rotamer: Outliers : 8.83 % Allowed : 19.43 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.40 (0.34), residues: 431 helix: -1.78 (0.62), residues: 61 sheet: -0.29 (1.09), residues: 28 loop : -3.76 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 57 HIS 0.002 0.001 HIS P 415 PHE 0.010 0.001 PHE P 261 TYR 0.014 0.002 TYR P 218 ARG 0.003 0.000 ARG P 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 59 time to evaluate : 0.204 Fit side-chains REVERT: P 30 TYR cc_start: 0.3611 (OUTLIER) cc_final: 0.3206 (m-10) REVERT: P 37 GLN cc_start: 0.8571 (pm20) cc_final: 0.8064 (pm20) REVERT: P 71 ARG cc_start: 0.7700 (mtm110) cc_final: 0.7407 (ttm110) REVERT: P 154 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6352 (pm20) REVERT: P 198 LYS cc_start: 0.8368 (ttpp) cc_final: 0.6771 (tppt) REVERT: P 263 LYS cc_start: 0.7747 (pttm) cc_final: 0.7480 (ptmm) REVERT: P 265 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.6535 (t-90) REVERT: P 395 ASN cc_start: 0.4398 (t0) cc_final: 0.3778 (p0) REVERT: P 396 GLU cc_start: 0.6565 (mm-30) cc_final: 0.6042 (tm-30) REVERT: P 431 ASN cc_start: 0.8061 (m110) cc_final: 0.7329 (t0) REVERT: P 454 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6930 (ptm-80) REVERT: P 458 VAL cc_start: 0.6332 (OUTLIER) cc_final: 0.6103 (t) outliers start: 25 outliers final: 15 residues processed: 78 average time/residue: 0.0947 time to fit residues: 8.9947 Evaluate side-chains 77 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 57 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 265 HIS Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 38 optimal weight: 0.0980 chunk 25 optimal weight: 0.0060 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.3598 ------------------------------------------------------------------------------- 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: 0.6486 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3148 Z= 0.149 Angle : 0.704 13.484 4286 Z= 0.354 Chirality : 0.042 0.139 504 Planarity : 0.006 0.080 564 Dihedral : 6.165 23.604 459 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.70 % Allowed : 12.53 % Favored : 86.77 % Rotamer: Outliers : 6.71 % Allowed : 21.91 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.34), residues: 431 helix: -1.50 (0.63), residues: 61 sheet: 0.26 (1.40), residues: 18 loop : -3.64 (0.26), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 57 HIS 0.002 0.000 HIS P 415 PHE 0.009 0.001 PHE P 261 TYR 0.010 0.001 TYR P 441 ARG 0.004 0.000 ARG P 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 58 time to evaluate : 0.204 Fit side-chains REVERT: P 30 TYR cc_start: 0.3473 (OUTLIER) cc_final: 0.2889 (m-10) REVERT: P 37 GLN cc_start: 0.8539 (pm20) cc_final: 0.7947 (pm20) REVERT: P 71 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7358 (ttm110) REVERT: P 263 LYS cc_start: 0.7409 (pttm) cc_final: 0.7177 (ptmm) REVERT: P 395 ASN cc_start: 0.4319 (t0) cc_final: 0.3877 (p0) REVERT: P 396 GLU cc_start: 0.6577 (mm-30) cc_final: 0.6050 (tm-30) REVERT: P 431 ASN cc_start: 0.8050 (m110) cc_final: 0.7356 (t0) REVERT: P 454 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6758 (ptm-80) REVERT: P 458 VAL cc_start: 0.6310 (OUTLIER) cc_final: 0.6069 (t) outliers start: 19 outliers final: 15 residues processed: 73 average time/residue: 0.0993 time to fit residues: 8.8028 Evaluate side-chains 72 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.6583 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3148 Z= 0.203 Angle : 0.752 13.269 4286 Z= 0.382 Chirality : 0.044 0.149 504 Planarity : 0.006 0.083 564 Dihedral : 6.515 23.976 459 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.70 % Allowed : 15.55 % Favored : 83.76 % Rotamer: Outliers : 8.13 % Allowed : 21.91 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 22.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.34), residues: 431 helix: -1.69 (0.62), residues: 61 sheet: -0.25 (1.10), residues: 28 loop : -3.65 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 57 HIS 0.002 0.001 HIS P 265 PHE 0.013 0.002 PHE P 261 TYR 0.023 0.002 TYR P 218 ARG 0.004 0.000 ARG P 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 59 time to evaluate : 0.205 Fit side-chains REVERT: P 30 TYR cc_start: 0.3629 (OUTLIER) cc_final: 0.3053 (m-80) REVERT: P 37 GLN cc_start: 0.8524 (pm20) cc_final: 0.8003 (pm20) REVERT: P 71 ARG cc_start: 0.7770 (mtm110) cc_final: 0.7474 (ttm110) REVERT: P 154 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6005 (pm20) REVERT: P 265 HIS cc_start: 0.7048 (OUTLIER) cc_final: 0.6657 (t-90) REVERT: P 395 ASN cc_start: 0.4245 (t0) cc_final: 0.3443 (p0) REVERT: P 431 ASN cc_start: 0.8176 (m110) cc_final: 0.7420 (t0) REVERT: P 454 ARG cc_start: 0.7263 (OUTLIER) cc_final: 0.6890 (ptm-80) REVERT: P 458 VAL cc_start: 0.6338 (OUTLIER) cc_final: 0.6111 (t) outliers start: 23 outliers final: 16 residues processed: 76 average time/residue: 0.0867 time to fit residues: 8.1280 Evaluate side-chains 76 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 55 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 30 TYR Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 92 SER Chi-restraints excluded: chain P residue 94 PHE Chi-restraints excluded: chain P residue 95 VAL Chi-restraints excluded: chain P residue 103 VAL Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain P residue 117 TYR Chi-restraints excluded: chain P residue 126 ILE Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 165 THR Chi-restraints excluded: chain P residue 188 ILE Chi-restraints excluded: chain P residue 257 SER Chi-restraints excluded: chain P residue 265 HIS Chi-restraints excluded: chain P residue 439 LEU Chi-restraints excluded: chain P residue 454 ARG Chi-restraints excluded: chain P residue 455 ILE Chi-restraints excluded: chain P residue 458 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 69.7831 > 50: distance: 8 - 11: 28.217 distance: 11 - 12: 11.076 distance: 12 - 13: 30.648 distance: 12 - 15: 29.019 distance: 13 - 14: 17.446 distance: 13 - 16: 59.553 distance: 16 - 17: 69.783 distance: 17 - 18: 45.877 distance: 17 - 20: 26.073 distance: 18 - 19: 20.778 distance: 18 - 21: 56.598 distance: 21 - 22: 24.246 distance: 22 - 23: 42.252 distance: 22 - 25: 24.351 distance: 23 - 24: 34.140 distance: 23 - 26: 27.088 distance: 26 - 27: 27.184 distance: 27 - 28: 27.101 distance: 27 - 30: 20.352 distance: 28 - 29: 7.893 distance: 28 - 31: 25.630 distance: 31 - 32: 19.412 distance: 32 - 33: 18.527 distance: 32 - 35: 39.834 distance: 33 - 34: 27.066 distance: 33 - 36: 13.307 distance: 36 - 37: 56.170 distance: 37 - 38: 49.691 distance: 37 - 40: 42.824 distance: 38 - 39: 40.203 distance: 38 - 41: 43.445 distance: 41 - 42: 31.677 distance: 42 - 43: 37.605 distance: 42 - 45: 6.319 distance: 43 - 44: 54.295 distance: 43 - 46: 18.456 distance: 46 - 47: 41.869 distance: 47 - 48: 28.418 distance: 47 - 50: 9.284 distance: 48 - 49: 31.953 distance: 48 - 51: 20.508 distance: 51 - 52: 38.356 distance: 52 - 53: 23.152 distance: 52 - 55: 44.995 distance: 53 - 54: 18.676 distance: 53 - 56: 17.550 distance: 56 - 57: 35.964 distance: 57 - 58: 35.335 distance: 58 - 59: 29.639 distance: 58 - 61: 21.629