Starting phenix.real_space_refine on Mon Sep 23 14:07:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x83_33054/09_2024/7x83_33054.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x83_33054/09_2024/7x83_33054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x83_33054/09_2024/7x83_33054.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x83_33054/09_2024/7x83_33054.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x83_33054/09_2024/7x83_33054.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x83_33054/09_2024/7x83_33054.cif" } resolution = 3.4 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= 0.001 sd= 0.003 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 21 5.16 5 C 2082 2.51 5 N 519 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Restraints were copied for chains: C, B Time building chain proxies: 2.52, per 1000 atoms: 0.77 Number of scatterers: 3258 At special positions: 0 Unit cell: (100.43, 100.43, 35.69, 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 21 16.00 O 636 8.00 N 519 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.705A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 137 removed outlier: 6.653A pdb=" N SER B 134 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N VAL C 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASP B 136 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 144 removed outlier: 6.553A pdb=" N TYR B 143 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151 removed outlier: 6.958A pdb=" N LEU B 150 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 156 removed outlier: 6.509A pdb=" N ASN B 155 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 163 through 164 removed outlier: 6.916A pdb=" N GLU B 163 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 167 through 169 removed outlier: 6.584A pdb=" N GLN B 168 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 186 removed outlier: 6.541A pdb=" N THR B 185 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 192 removed outlier: 6.479A pdb=" N LEU B 190 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 201 through 213 removed outlier: 8.933A pdb=" N VAL B 202 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N GLU A 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA B 204 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N MET A 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU B 206 " --> pdb=" O MET A 207 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR A 209 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER B 208 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N TYR A 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET B 210 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N PHE A 213 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 212 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C 202 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 203 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA C 204 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 216 through 219 removed outlier: 5.914A pdb=" N LEU B 216 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE C 219 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER B 218 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 222 through 230 removed outlier: 6.990A pdb=" N VAL B 230 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN B 223 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU C 226 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N MET C 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET B 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL C 230 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLN B 229 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 240 through 244 removed outlier: 6.646A pdb=" N SER B 240 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ILE C 243 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN B 242 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 251 through 253 removed outlier: 6.458A pdb=" N ASP B 252 " --> pdb=" O CYS A 253 " (cutoff:3.500A) 41 hydrogen bonds defined for protein. 123 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: 0.74 Time building geometry restraints manager: 0.89 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: 1026 1.34 - 1.45: 538 1.45 - 1.57: 1712 1.57 - 1.69: 0 1.69 - 1.80: 36 Bond restraints: 3312 Sorted by residual: bond pdb=" CA VAL B 230 " pdb=" C VAL B 230 " ideal model delta sigma weight residual 1.527 1.513 0.014 8.50e-03 1.38e+04 2.73e+00 bond pdb=" CA ARG B 247 " pdb=" C ARG B 247 " ideal model delta sigma weight residual 1.531 1.514 0.017 1.08e-02 8.57e+03 2.46e+00 bond pdb=" CA ARG A 247 " pdb=" C ARG A 247 " ideal model delta sigma weight residual 1.531 1.515 0.017 1.08e-02 8.57e+03 2.34e+00 bond pdb=" CA VAL C 230 " pdb=" C VAL C 230 " ideal model delta sigma weight residual 1.527 1.514 0.013 8.50e-03 1.38e+04 2.34e+00 bond pdb=" CA ARG C 247 " pdb=" C ARG C 247 " ideal model delta sigma weight residual 1.531 1.515 0.016 1.08e-02 8.57e+03 2.33e+00 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 3790 1.03 - 2.06: 559 2.06 - 3.09: 121 3.09 - 4.12: 21 4.12 - 5.16: 12 Bond angle restraints: 4503 Sorted by residual: angle pdb=" C GLN C 245 " pdb=" N GLU C 246 " pdb=" CA GLU C 246 " ideal model delta sigma weight residual 122.11 117.17 4.94 1.59e+00 3.96e-01 9.66e+00 angle pdb=" C GLN B 245 " pdb=" N GLU B 246 " pdb=" CA GLU B 246 " ideal model delta sigma weight residual 122.11 117.17 4.94 1.59e+00 3.96e-01 9.66e+00 angle pdb=" C GLN A 245 " pdb=" N GLU A 246 " pdb=" CA GLU A 246 " ideal model delta sigma weight residual 122.11 117.21 4.90 1.59e+00 3.96e-01 9.50e+00 angle pdb=" C LEU A 144 " pdb=" N ASN A 145 " pdb=" CA ASN A 145 " ideal model delta sigma weight residual 121.54 126.70 -5.16 1.91e+00 2.74e-01 7.28e+00 angle pdb=" CA TYR C 143 " pdb=" CB TYR C 143 " pdb=" CG TYR C 143 " ideal model delta sigma weight residual 113.90 118.75 -4.85 1.80e+00 3.09e-01 7.27e+00 ... (remaining 4498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 1788 16.36 - 32.72: 175 32.72 - 49.08: 17 49.08 - 65.43: 6 65.43 - 81.79: 3 Dihedral angle restraints: 1989 sinusoidal: 771 harmonic: 1218 Sorted by residual: dihedral pdb=" CA GLN C 138 " pdb=" C GLN C 138 " pdb=" N LYS C 139 " pdb=" CA LYS C 139 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA GLN A 138 " pdb=" C GLN A 138 " pdb=" N LYS A 139 " pdb=" CA LYS A 139 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLN B 138 " pdb=" C GLN B 138 " pdb=" N LYS B 139 " pdb=" CA LYS B 139 " ideal model delta harmonic sigma weight residual 180.00 158.00 22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 1986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 255 0.035 - 0.071: 156 0.071 - 0.106: 88 0.106 - 0.142: 35 0.142 - 0.177: 9 Chirality restraints: 543 Sorted by residual: chirality pdb=" CA ASN A 145 " pdb=" N ASN A 145 " pdb=" C ASN A 145 " pdb=" CB ASN A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA ASN C 145 " pdb=" N ASN C 145 " pdb=" C ASN C 145 " pdb=" CB ASN C 145 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CA ASN B 145 " pdb=" N ASN B 145 " pdb=" C ASN B 145 " pdb=" CB ASN B 145 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 540 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 143 " 0.018 2.00e-02 2.50e+03 1.14e-02 2.60e+00 pdb=" CG TYR A 143 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 143 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 143 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 143 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 143 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 143 " 0.018 2.00e-02 2.50e+03 1.13e-02 2.56e+00 pdb=" CG TYR C 143 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR C 143 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR C 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 143 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 143 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 143 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 143 " 0.018 2.00e-02 2.50e+03 1.12e-02 2.51e+00 pdb=" CG TYR B 143 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 143 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 143 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 143 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 143 " 0.004 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 30 2.60 - 3.18: 2875 3.18 - 3.75: 4567 3.75 - 4.33: 6568 4.33 - 4.90: 12143 Nonbonded interactions: 26183 Sorted by model distance: nonbonded pdb=" SG CYS A 214 " pdb=" SG CYS A 253 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " model vdw 2.028 3.760 nonbonded pdb=" OH TYR B 236 " pdb=" OG SER B 240 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 236 " pdb=" OG SER A 240 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR C 236 " pdb=" OG SER C 240 " model vdw 2.218 3.040 ... (remaining 26178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.600 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 : 0.009 0.058 3312 Z= 0.585 Angle : 0.825 5.155 4503 Z= 0.494 Chirality : 0.060 0.177 543 Planarity : 0.003 0.011 558 Dihedral : 13.347 81.792 1206 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.71 (0.28), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.22), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 222 PHE 0.010 0.003 PHE A 213 TYR 0.026 0.003 TYR A 143 ARG 0.003 0.001 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.375 Fit side-chains REVERT: B 140 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7233 (ttm110) REVERT: B 178 LYS cc_start: 0.7339 (mttt) cc_final: 0.6399 (tptt) REVERT: B 215 THR cc_start: 0.7671 (t) cc_final: 0.7398 (t) REVERT: A 140 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7490 (ttm110) REVERT: A 178 LYS cc_start: 0.7850 (mttt) cc_final: 0.6991 (tptt) REVERT: C 140 ARG cc_start: 0.7745 (mtt180) cc_final: 0.7510 (ttm110) REVERT: C 178 LYS cc_start: 0.7310 (mttt) cc_final: 0.6486 (tptt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2501 time to fit residues: 14.4004 Evaluate side-chains 37 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 156 ASN B 223 ASN A 156 ASN A 223 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 223 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3312 Z= 0.265 Angle : 0.612 5.443 4503 Z= 0.340 Chirality : 0.054 0.183 543 Planarity : 0.002 0.020 558 Dihedral : 6.646 19.261 447 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer: Outliers : 3.70 % Allowed : 12.17 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.42 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.009 0.002 PHE A 237 TYR 0.019 0.002 TYR B 143 ARG 0.001 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.387 Fit side-chains REVERT: B 140 ARG cc_start: 0.7722 (mtt180) cc_final: 0.7358 (ttm110) REVERT: B 145 ASN cc_start: 0.7395 (p0) cc_final: 0.7184 (p0) REVERT: B 146 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8233 (pt) REVERT: B 178 LYS cc_start: 0.7395 (mttt) cc_final: 0.6539 (tptt) REVERT: B 215 THR cc_start: 0.7876 (t) cc_final: 0.7595 (t) REVERT: A 140 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7625 (ttm110) REVERT: A 178 LYS cc_start: 0.7674 (mttt) cc_final: 0.6927 (tptt) REVERT: C 140 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7599 (ttm110) REVERT: C 145 ASN cc_start: 0.7641 (p0) cc_final: 0.7241 (p0) REVERT: C 146 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8016 (pt) REVERT: C 178 LYS cc_start: 0.7279 (mttt) cc_final: 0.6532 (tptt) outliers start: 14 outliers final: 6 residues processed: 55 average time/residue: 0.1785 time to fit residues: 11.9233 Evaluate side-chains 49 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 175 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 0.0270 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3312 Z= 0.150 Angle : 0.537 5.923 4503 Z= 0.294 Chirality : 0.051 0.175 543 Planarity : 0.002 0.012 558 Dihedral : 5.826 15.640 447 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 3.70 % Allowed : 13.49 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.17 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.008 0.001 PHE A 237 TYR 0.011 0.001 TYR B 143 ARG 0.001 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.362 Fit side-chains REVERT: B 140 ARG cc_start: 0.7811 (mtt180) cc_final: 0.7491 (ttm110) REVERT: B 145 ASN cc_start: 0.7399 (p0) cc_final: 0.7143 (p0) REVERT: B 146 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8154 (pt) REVERT: B 178 LYS cc_start: 0.7417 (mttt) cc_final: 0.6635 (tptt) REVERT: B 215 THR cc_start: 0.7692 (t) cc_final: 0.7454 (t) REVERT: A 140 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7674 (ttm110) REVERT: A 146 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8136 (pt) REVERT: A 178 LYS cc_start: 0.7435 (mttt) cc_final: 0.6799 (tptt) REVERT: C 145 ASN cc_start: 0.7768 (p0) cc_final: 0.7361 (p0) REVERT: C 146 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8109 (pt) REVERT: C 178 LYS cc_start: 0.7298 (mttt) cc_final: 0.6572 (tptt) outliers start: 14 outliers final: 6 residues processed: 60 average time/residue: 0.1985 time to fit residues: 14.0869 Evaluate side-chains 47 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3312 Z= 0.223 Angle : 0.564 6.218 4503 Z= 0.309 Chirality : 0.052 0.179 543 Planarity : 0.002 0.012 558 Dihedral : 5.835 15.684 447 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 5.29 % Allowed : 13.76 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.07 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.010 0.002 PHE A 237 TYR 0.016 0.002 TYR B 143 ARG 0.005 0.001 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 45 time to evaluate : 0.362 Fit side-chains REVERT: B 140 ARG cc_start: 0.7788 (mtt180) cc_final: 0.7488 (ttm110) REVERT: B 145 ASN cc_start: 0.7340 (p0) cc_final: 0.7100 (p0) REVERT: B 146 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8151 (pt) REVERT: B 178 LYS cc_start: 0.7333 (mttt) cc_final: 0.6485 (tptt) REVERT: B 209 TYR cc_start: 0.6966 (m-80) cc_final: 0.6418 (m-80) REVERT: B 215 THR cc_start: 0.7750 (t) cc_final: 0.7518 (t) REVERT: A 140 ARG cc_start: 0.7918 (mtt180) cc_final: 0.7714 (ttm110) REVERT: A 178 LYS cc_start: 0.7489 (mttt) cc_final: 0.6796 (tptt) REVERT: C 145 ASN cc_start: 0.7890 (p0) cc_final: 0.7423 (p0) REVERT: C 146 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8011 (pt) REVERT: C 178 LYS cc_start: 0.7269 (mttt) cc_final: 0.6512 (tptt) REVERT: C 209 TYR cc_start: 0.7084 (m-80) cc_final: 0.6807 (m-80) outliers start: 20 outliers final: 12 residues processed: 63 average time/residue: 0.1736 time to fit residues: 13.3906 Evaluate side-chains 55 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 41 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 239 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 3312 Z= 0.578 Angle : 0.761 6.275 4503 Z= 0.429 Chirality : 0.060 0.197 543 Planarity : 0.003 0.020 558 Dihedral : 6.804 21.208 447 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer: Outliers : 5.82 % Allowed : 12.96 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.40 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS B 222 PHE 0.018 0.003 PHE A 237 TYR 0.030 0.003 TYR A 143 ARG 0.003 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 45 time to evaluate : 0.395 Fit side-chains REVERT: B 140 ARG cc_start: 0.7680 (mtt180) cc_final: 0.7471 (ttm110) REVERT: B 145 ASN cc_start: 0.7368 (p0) cc_final: 0.6930 (p0) REVERT: B 178 LYS cc_start: 0.7518 (mttt) cc_final: 0.6491 (tptt) REVERT: A 140 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7642 (ttm110) REVERT: A 178 LYS cc_start: 0.7686 (mttt) cc_final: 0.6861 (tptt) REVERT: C 145 ASN cc_start: 0.7775 (p0) cc_final: 0.7337 (p0) REVERT: C 178 LYS cc_start: 0.7298 (mttt) cc_final: 0.6404 (tptt) REVERT: C 207 MET cc_start: 0.7271 (ttm) cc_final: 0.6892 (ttt) outliers start: 22 outliers final: 19 residues processed: 66 average time/residue: 0.1388 time to fit residues: 11.3485 Evaluate side-chains 58 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 39 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.0470 chunk 36 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3312 Z= 0.226 Angle : 0.590 5.374 4503 Z= 0.325 Chirality : 0.054 0.192 543 Planarity : 0.002 0.010 558 Dihedral : 6.149 16.241 447 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 4.50 % Allowed : 15.08 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.16 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 239 PHE 0.013 0.002 PHE A 213 TYR 0.017 0.002 TYR B 143 ARG 0.003 0.001 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 0.375 Fit side-chains REVERT: B 140 ARG cc_start: 0.7854 (mtt180) cc_final: 0.7479 (ttm110) REVERT: B 146 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8185 (pt) REVERT: B 178 LYS cc_start: 0.7511 (mttt) cc_final: 0.6661 (tptt) REVERT: B 209 TYR cc_start: 0.6945 (m-80) cc_final: 0.6393 (m-80) REVERT: A 140 ARG cc_start: 0.7914 (mtt180) cc_final: 0.7629 (ttm110) REVERT: A 178 LYS cc_start: 0.7549 (mttt) cc_final: 0.6784 (tptt) REVERT: C 145 ASN cc_start: 0.7787 (p0) cc_final: 0.7341 (p0) REVERT: C 146 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8048 (pt) REVERT: C 171 PHE cc_start: 0.8384 (m-80) cc_final: 0.8156 (m-80) REVERT: C 178 LYS cc_start: 0.7319 (mttt) cc_final: 0.6558 (tptt) REVERT: C 209 TYR cc_start: 0.7350 (m-80) cc_final: 0.7103 (m-80) outliers start: 17 outliers final: 14 residues processed: 62 average time/residue: 0.1571 time to fit residues: 11.9094 Evaluate side-chains 60 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 37 optimal weight: 0.0270 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 15 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 overall best weight: 1.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3312 Z= 0.171 Angle : 0.554 6.228 4503 Z= 0.305 Chirality : 0.053 0.209 543 Planarity : 0.002 0.012 558 Dihedral : 5.658 14.781 447 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 4.76 % Allowed : 15.61 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.011 0.001 PHE A 213 TYR 0.019 0.001 TYR B 143 ARG 0.003 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 0.373 Fit side-chains REVERT: B 140 ARG cc_start: 0.7853 (mtt180) cc_final: 0.7547 (ttm110) REVERT: B 146 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8228 (pt) REVERT: B 178 LYS cc_start: 0.7370 (mttt) cc_final: 0.6552 (tptt) REVERT: A 178 LYS cc_start: 0.7422 (mttt) cc_final: 0.6800 (tptt) REVERT: C 145 ASN cc_start: 0.7619 (p0) cc_final: 0.7375 (t0) REVERT: C 146 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8138 (pt) REVERT: C 171 PHE cc_start: 0.8347 (m-80) cc_final: 0.8144 (m-80) REVERT: C 178 LYS cc_start: 0.7320 (mttt) cc_final: 0.6534 (tptt) outliers start: 18 outliers final: 14 residues processed: 58 average time/residue: 0.1703 time to fit residues: 11.9234 Evaluate side-chains 54 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 38 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3312 Z= 0.294 Angle : 0.613 6.202 4503 Z= 0.340 Chirality : 0.055 0.215 543 Planarity : 0.003 0.053 558 Dihedral : 6.009 16.768 447 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % Rotamer: Outliers : 4.23 % Allowed : 16.40 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 239 PHE 0.011 0.002 PHE A 213 TYR 0.019 0.002 TYR B 143 ARG 0.011 0.001 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 49 time to evaluate : 0.388 Fit side-chains REVERT: B 140 ARG cc_start: 0.7854 (mtt180) cc_final: 0.7543 (ttm110) REVERT: B 146 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8228 (pt) REVERT: B 178 LYS cc_start: 0.7466 (mttt) cc_final: 0.6561 (tptt) REVERT: B 209 TYR cc_start: 0.6918 (m-80) cc_final: 0.6380 (m-80) REVERT: A 178 LYS cc_start: 0.7541 (mttt) cc_final: 0.6783 (tptt) REVERT: C 145 ASN cc_start: 0.7798 (p0) cc_final: 0.7564 (p0) REVERT: C 146 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8142 (pt) REVERT: C 171 PHE cc_start: 0.8401 (m-80) cc_final: 0.8174 (m-80) REVERT: C 178 LYS cc_start: 0.7329 (mttt) cc_final: 0.6508 (tptt) outliers start: 16 outliers final: 14 residues processed: 61 average time/residue: 0.1443 time to fit residues: 10.9813 Evaluate side-chains 60 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3312 Z= 0.155 Angle : 0.544 6.401 4503 Z= 0.300 Chirality : 0.053 0.228 543 Planarity : 0.003 0.043 558 Dihedral : 5.540 14.496 447 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 4.23 % Allowed : 17.46 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.009 0.001 PHE A 213 TYR 0.014 0.001 TYR B 143 ARG 0.011 0.001 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.358 Fit side-chains REVERT: B 146 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8304 (pt) REVERT: B 178 LYS cc_start: 0.7373 (mttt) cc_final: 0.6604 (tptt) REVERT: A 178 LYS cc_start: 0.7401 (mttt) cc_final: 0.6772 (tptt) REVERT: C 146 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8156 (pt) REVERT: C 171 PHE cc_start: 0.8330 (m-80) cc_final: 0.8130 (m-80) REVERT: C 178 LYS cc_start: 0.7371 (mttt) cc_final: 0.6551 (tptt) outliers start: 16 outliers final: 12 residues processed: 58 average time/residue: 0.1563 time to fit residues: 11.0482 Evaluate side-chains 53 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.0570 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3312 Z= 0.333 Angle : 0.641 6.294 4503 Z= 0.356 Chirality : 0.055 0.239 543 Planarity : 0.003 0.041 558 Dihedral : 6.058 17.490 447 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.79 % Favored : 85.21 % Rotamer: Outliers : 4.23 % Allowed : 16.93 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.87 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 239 PHE 0.011 0.002 PHE A 237 TYR 0.022 0.002 TYR A 143 ARG 0.010 0.001 ARG A 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 41 time to evaluate : 0.391 Fit side-chains REVERT: B 178 LYS cc_start: 0.7503 (mttt) cc_final: 0.6613 (tptt) REVERT: B 209 TYR cc_start: 0.6787 (m-80) cc_final: 0.6305 (m-80) REVERT: A 178 LYS cc_start: 0.7545 (mttt) cc_final: 0.6762 (tptt) REVERT: C 146 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8120 (pt) REVERT: C 171 PHE cc_start: 0.8414 (m-80) cc_final: 0.8170 (m-80) REVERT: C 178 LYS cc_start: 0.7386 (mttt) cc_final: 0.6498 (tptt) outliers start: 16 outliers final: 13 residues processed: 53 average time/residue: 0.1368 time to fit residues: 9.2202 Evaluate side-chains 53 residues out of total 378 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 39 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 62.3709 > 50: distance: 0 - 97: 3.075 distance: 27 - 134: 22.582 distance: 42 - 137: 31.581 distance: 45 - 150: 23.840 distance: 57 - 153: 6.288 distance: 60 - 165: 28.421 distance: 72 - 168: 26.239 distance: 96 - 100: 11.552 distance: 100 - 101: 13.916 distance: 101 - 102: 7.584 distance: 101 - 104: 11.372 distance: 102 - 103: 23.356 distance: 102 - 108: 6.873 distance: 104 - 105: 17.320 distance: 104 - 106: 9.286 distance: 105 - 107: 15.190 distance: 108 - 109: 9.148 distance: 109 - 110: 3.237 distance: 109 - 112: 9.526 distance: 110 - 111: 15.400 distance: 110 - 117: 9.784 distance: 112 - 113: 4.837 distance: 114 - 115: 11.808 distance: 115 - 116: 4.941 distance: 117 - 118: 6.062 distance: 118 - 119: 26.684 distance: 118 - 121: 4.667 distance: 119 - 120: 27.934 distance: 119 - 124: 27.656 distance: 121 - 122: 16.724 distance: 121 - 123: 34.877 distance: 124 - 125: 26.003 distance: 125 - 126: 25.164 distance: 125 - 128: 24.974 distance: 126 - 127: 25.211 distance: 126 - 134: 18.845 distance: 128 - 129: 30.271 distance: 129 - 130: 15.669 distance: 129 - 131: 44.119 distance: 130 - 132: 7.568 distance: 131 - 133: 25.070 distance: 132 - 133: 33.142 distance: 134 - 135: 24.262 distance: 135 - 136: 27.224 distance: 135 - 138: 33.325 distance: 136 - 137: 10.810 distance: 136 - 142: 13.079 distance: 138 - 139: 3.262 distance: 139 - 140: 3.093 distance: 139 - 141: 8.489 distance: 142 - 143: 10.054 distance: 143 - 144: 45.793 distance: 143 - 146: 25.889 distance: 144 - 145: 58.809 distance: 144 - 150: 31.413 distance: 146 - 147: 16.476 distance: 146 - 148: 17.646 distance: 147 - 149: 21.341 distance: 150 - 151: 14.409 distance: 151 - 152: 35.190 distance: 151 - 154: 12.735 distance: 152 - 153: 14.858 distance: 152 - 157: 20.284 distance: 154 - 155: 24.951 distance: 154 - 156: 38.444 distance: 157 - 158: 23.382 distance: 158 - 159: 27.685 distance: 158 - 161: 18.103 distance: 159 - 165: 61.735 distance: 161 - 162: 21.772 distance: 162 - 163: 21.261 distance: 165 - 166: 12.515 distance: 166 - 167: 33.517 distance: 166 - 169: 35.043 distance: 167 - 168: 28.648 distance: 167 - 173: 22.208 distance: 169 - 170: 5.779 distance: 170 - 171: 26.489 distance: 171 - 172: 40.348 distance: 173 - 174: 5.032 distance: 174 - 175: 7.389 distance: 174 - 177: 23.932 distance: 175 - 176: 25.379 distance: 175 - 181: 10.067 distance: 177 - 178: 10.703 distance: 178 - 179: 20.924 distance: 179 - 180: 8.820