Starting phenix.real_space_refine on Mon Jan 13 20:24:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjq_37589/01_2025/8wjq_37589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjq_37589/01_2025/8wjq_37589.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/cci-nas-00/data/ceres_data/8wjq_37589/01_2025/8wjq_37589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjq_37589/01_2025/8wjq_37589.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjq_37589/01_2025/8wjq_37589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjq_37589/01_2025/8wjq_37589.cif" } 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= 0.002 sd= 0.060 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 30 5.16 5 C 2599 2.51 5 N 676 2.21 5 O 694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3999 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3987 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 29, 'TRANS': 500} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.62, per 1000 atoms: 0.66 Number of scatterers: 3999 At special positions: 0 Unit cell: (107, 85.6, 67.41, 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 30 16.00 O 694 8.00 N 676 7.00 C 2599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 139 " distance=2.04 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: 1.06 Conformation dependent library (CDL) restraints added in 500.5 milliseconds 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 2 sheets defined 83.2% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 14 through 41 removed outlier: 3.526A pdb=" N VAL A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.802A pdb=" N ARG A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 130 through 136 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 143 through 171 Proline residue: A 165 - end of helix Processing helix chain 'A' and resid 171 through 192 Processing helix chain 'A' and resid 195 through 225 removed outlier: 3.519A pdb=" N ALA A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 255 Processing helix chain 'A' and resid 257 through 277 Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 291 through 306 Processing helix chain 'A' and resid 308 through 314 removed outlier: 3.662A pdb=" N THR A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 removed outlier: 4.309A pdb=" N GLU A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 removed outlier: 3.512A pdb=" N LEU A 340 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 368 Processing helix chain 'A' and resid 369 through 375 removed outlier: 3.574A pdb=" N GLY A 375 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 404 through 426 removed outlier: 3.756A pdb=" N THR A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 460 removed outlier: 4.046A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 490 removed outlier: 4.356A pdb=" N MET A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N THR A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 494 through 513 removed outlier: 4.613A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 526 through 538 removed outlier: 3.603A pdb=" N VAL A 530 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 531 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN A 532 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.737A pdb=" N ARG A 48 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 90 308 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 620 1.32 - 1.45: 1117 1.45 - 1.58: 2311 1.58 - 1.71: 3 1.71 - 1.84: 48 Bond restraints: 4099 Sorted by residual: bond pdb=" CG PRO A 146 " pdb=" CD PRO A 146 " ideal model delta sigma weight residual 1.503 1.234 0.269 3.40e-02 8.65e+02 6.24e+01 bond pdb=" CG PRO A 194 " pdb=" CD PRO A 194 " ideal model delta sigma weight residual 1.503 1.280 0.223 3.40e-02 8.65e+02 4.30e+01 bond pdb=" C4 URC A 601 " pdb=" N9 URC A 601 " ideal model delta sigma weight residual 1.352 1.479 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" N PRO A 146 " pdb=" CD PRO A 146 " ideal model delta sigma weight residual 1.473 1.552 -0.079 1.40e-02 5.10e+03 3.18e+01 bond pdb=" C4 URC A 601 " pdb=" N3 URC A 601 " ideal model delta sigma weight residual 1.352 1.464 -0.112 2.00e-02 2.50e+03 3.14e+01 ... (remaining 4094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 5450 3.91 - 7.81: 115 7.81 - 11.72: 28 11.72 - 15.62: 6 15.62 - 19.53: 2 Bond angle restraints: 5601 Sorted by residual: angle pdb=" CA PRO A 146 " pdb=" N PRO A 146 " pdb=" CD PRO A 146 " ideal model delta sigma weight residual 112.00 92.47 19.53 1.40e+00 5.10e-01 1.95e+02 angle pdb=" CA PRO A 194 " pdb=" N PRO A 194 " pdb=" CD PRO A 194 " ideal model delta sigma weight residual 112.00 94.02 17.98 1.40e+00 5.10e-01 1.65e+02 angle pdb=" N PRO A 146 " pdb=" CD PRO A 146 " pdb=" CG PRO A 146 " ideal model delta sigma weight residual 103.20 90.41 12.79 1.50e+00 4.44e-01 7.27e+01 angle pdb=" CA GLU A 114 " pdb=" CB GLU A 114 " pdb=" CG GLU A 114 " ideal model delta sigma weight residual 114.10 129.04 -14.94 2.00e+00 2.50e-01 5.58e+01 angle pdb=" N PRO A 194 " pdb=" CD PRO A 194 " pdb=" CG PRO A 194 " ideal model delta sigma weight residual 103.20 92.88 10.32 1.50e+00 4.44e-01 4.74e+01 ... (remaining 5596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 2110 16.85 - 33.70: 188 33.70 - 50.55: 80 50.55 - 67.40: 13 67.40 - 84.25: 2 Dihedral angle restraints: 2393 sinusoidal: 885 harmonic: 1508 Sorted by residual: dihedral pdb=" CA MET A 36 " pdb=" C MET A 36 " pdb=" N LEU A 37 " pdb=" CA LEU A 37 " ideal model delta harmonic sigma weight residual 180.00 152.11 27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sinusoidal sigma weight residual 93.00 137.60 -44.60 1 1.00e+01 1.00e-02 2.76e+01 dihedral pdb=" N ARG A 92 " pdb=" C ARG A 92 " pdb=" CA ARG A 92 " pdb=" CB ARG A 92 " ideal model delta harmonic sigma weight residual 122.80 135.35 -12.55 0 2.50e+00 1.60e-01 2.52e+01 ... (remaining 2390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 583 0.099 - 0.198: 70 0.198 - 0.296: 6 0.296 - 0.395: 1 0.395 - 0.494: 1 Chirality restraints: 661 Sorted by residual: chirality pdb=" CB THR A 453 " pdb=" CA THR A 453 " pdb=" OG1 THR A 453 " pdb=" CG2 THR A 453 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CA ARG A 92 " pdb=" N ARG A 92 " pdb=" C ARG A 92 " pdb=" CB ARG A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 chirality pdb=" CA THR A 453 " pdb=" N THR A 453 " pdb=" C THR A 453 " pdb=" CB THR A 453 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 658 not shown) Planarity restraints: 697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 193 " -0.150 5.00e-02 4.00e+02 2.07e-01 6.89e+01 pdb=" N PRO A 194 " 0.358 5.00e-02 4.00e+02 pdb=" CA PRO A 194 " -0.115 5.00e-02 4.00e+02 pdb=" CD PRO A 194 " -0.092 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 145 " 0.135 5.00e-02 4.00e+02 1.84e-01 5.43e+01 pdb=" N PRO A 146 " -0.318 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.093 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 135 " 0.048 2.00e-02 2.50e+03 3.82e-02 3.65e+01 pdb=" CG TRP A 135 " -0.102 2.00e-02 2.50e+03 pdb=" CD1 TRP A 135 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP A 135 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 135 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 135 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 135 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 135 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 135 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 135 " 0.006 2.00e-02 2.50e+03 ... (remaining 694 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 443 2.75 - 3.29: 4171 3.29 - 3.83: 6912 3.83 - 4.36: 7162 4.36 - 4.90: 12407 Nonbonded interactions: 31095 Sorted by model distance: nonbonded pdb=" O ALA A 359 " pdb=" OG1 THR A 363 " model vdw 2.216 3.040 nonbonded pdb=" O LEU A 221 " pdb=" OG1 THR A 225 " model vdw 2.253 3.040 nonbonded pdb=" O SER A 336 " pdb=" OG1 THR A 339 " model vdw 2.275 3.040 nonbonded pdb=" O TRP A 30 " pdb=" OG1 THR A 33 " model vdw 2.275 3.040 nonbonded pdb=" O TRP A 50 " pdb=" NH1 ARG A 90 " model vdw 2.284 3.120 ... (remaining 31090 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: 0.300 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.510 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5784 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 : 0.010 0.269 4099 Z= 0.633 Angle : 1.470 19.530 5601 Z= 0.789 Chirality : 0.066 0.494 661 Planarity : 0.018 0.207 697 Dihedral : 15.618 84.254 1415 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.48 % Allowed : 16.67 % Favored : 82.85 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.35), residues: 526 helix: 0.97 (0.25), residues: 408 sheet: None (None), residues: 0 loop : -0.79 (0.53), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.004 TRP A 135 HIS 0.016 0.003 HIS A 47 PHE 0.036 0.004 PHE A 348 TYR 0.027 0.006 TYR A 275 ARG 0.044 0.004 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.5901 (tpt) cc_final: 0.5642 (tpt) REVERT: A 324 MET cc_start: 0.6727 (mmm) cc_final: 0.6518 (mmm) REVERT: A 466 MET cc_start: 0.6760 (mmp) cc_final: 0.6249 (mmm) REVERT: A 531 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6813 (tm-30) outliers start: 2 outliers final: 0 residues processed: 74 average time/residue: 0.1442 time to fit residues: 13.9727 Evaluate side-chains 68 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.261681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.218583 restraints weight = 4807.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.225032 restraints weight = 2698.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.229449 restraints weight = 1794.286| |-----------------------------------------------------------------------------| r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4099 Z= 0.222 Angle : 0.708 9.784 5601 Z= 0.363 Chirality : 0.041 0.173 661 Planarity : 0.008 0.097 697 Dihedral : 4.319 16.853 561 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.14 % Allowed : 17.39 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.37), residues: 526 helix: 1.51 (0.26), residues: 413 sheet: None (None), residues: 0 loop : -0.42 (0.58), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 135 HIS 0.006 0.001 HIS A 86 PHE 0.017 0.002 PHE A 269 TYR 0.021 0.002 TYR A 275 ARG 0.004 0.001 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.409 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 86 average time/residue: 0.1210 time to fit residues: 13.8095 Evaluate side-chains 69 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 365 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.270134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.224392 restraints weight = 4772.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.231429 restraints weight = 2617.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.236060 restraints weight = 1705.644| |-----------------------------------------------------------------------------| r_work (final): 0.4483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4099 Z= 0.197 Angle : 0.675 11.615 5601 Z= 0.333 Chirality : 0.040 0.160 661 Planarity : 0.006 0.064 697 Dihedral : 4.253 15.133 561 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.66 % Allowed : 19.32 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.37), residues: 526 helix: 1.62 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -0.36 (0.58), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 135 HIS 0.005 0.001 HIS A 86 PHE 0.036 0.002 PHE A 269 TYR 0.016 0.002 TYR A 275 ARG 0.005 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 95 GLN cc_start: 0.7366 (tp40) cc_final: 0.6899 (tp-100) REVERT: A 324 MET cc_start: 0.6655 (mmm) cc_final: 0.6167 (mmm) outliers start: 11 outliers final: 7 residues processed: 75 average time/residue: 0.1452 time to fit residues: 14.1505 Evaluate side-chains 68 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 454 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.253729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.208078 restraints weight = 4833.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.214081 restraints weight = 2738.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.218350 restraints weight = 1852.103| |-----------------------------------------------------------------------------| r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4099 Z= 0.208 Angle : 0.645 11.554 5601 Z= 0.320 Chirality : 0.039 0.122 661 Planarity : 0.006 0.058 697 Dihedral : 4.194 14.997 561 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.14 % Allowed : 22.22 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.37), residues: 526 helix: 1.71 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -0.63 (0.57), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 357 HIS 0.003 0.001 HIS A 86 PHE 0.027 0.002 PHE A 269 TYR 0.016 0.002 TYR A 275 ARG 0.005 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 36 MET cc_start: 0.4934 (mmp) cc_final: 0.4437 (mmp) REVERT: A 95 GLN cc_start: 0.7684 (tp-100) cc_final: 0.7229 (tp40) REVERT: A 284 ARG cc_start: 0.7071 (ttm-80) cc_final: 0.6307 (ttm-80) REVERT: A 324 MET cc_start: 0.6573 (mmm) cc_final: 0.6331 (mmm) REVERT: A 428 HIS cc_start: 0.6098 (OUTLIER) cc_final: 0.5657 (t-90) REVERT: A 453 THR cc_start: 0.7095 (OUTLIER) cc_final: 0.5451 (p) REVERT: A 471 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7077 (tt) outliers start: 13 outliers final: 6 residues processed: 78 average time/residue: 0.1517 time to fit residues: 15.0493 Evaluate side-chains 70 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 471 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.252072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.206063 restraints weight = 4939.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.212267 restraints weight = 2778.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.216586 restraints weight = 1859.614| |-----------------------------------------------------------------------------| r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4099 Z= 0.191 Angle : 0.640 11.274 5601 Z= 0.313 Chirality : 0.039 0.118 661 Planarity : 0.006 0.059 697 Dihedral : 4.222 16.227 561 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.11 % Allowed : 23.67 % Favored : 72.22 % 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: 1.88 (0.37), residues: 526 helix: 1.80 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -0.68 (0.56), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 357 HIS 0.002 0.000 HIS A 47 PHE 0.024 0.002 PHE A 269 TYR 0.014 0.002 TYR A 275 ARG 0.005 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.7703 (tp-100) cc_final: 0.7468 (tp40) REVERT: A 284 ARG cc_start: 0.6985 (ttm-80) cc_final: 0.6216 (ttm-80) REVERT: A 324 MET cc_start: 0.6635 (mmm) cc_final: 0.6418 (mmm) REVERT: A 356 CYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8378 (t) REVERT: A 453 THR cc_start: 0.7048 (OUTLIER) cc_final: 0.5476 (p) REVERT: A 471 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7053 (tt) outliers start: 17 outliers final: 8 residues processed: 82 average time/residue: 0.1302 time to fit residues: 13.9979 Evaluate side-chains 78 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 6 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 0.0770 chunk 30 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 0.0470 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.252953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.207677 restraints weight = 4870.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.213932 restraints weight = 2778.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.218203 restraints weight = 1868.466| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4099 Z= 0.175 Angle : 0.638 11.187 5601 Z= 0.306 Chirality : 0.038 0.119 661 Planarity : 0.005 0.056 697 Dihedral : 4.193 14.645 561 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.86 % Allowed : 24.15 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.38), residues: 526 helix: 1.92 (0.26), residues: 407 sheet: None (None), residues: 0 loop : -0.93 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.002 0.000 HIS A 47 PHE 0.012 0.001 PHE A 358 TYR 0.013 0.002 TYR A 275 ARG 0.004 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.5541 (ttt180) cc_final: 0.5056 (ttt90) REVERT: A 95 GLN cc_start: 0.7729 (tp-100) cc_final: 0.7412 (tp40) REVERT: A 147 MET cc_start: 0.6340 (mtt) cc_final: 0.5920 (tpp) REVERT: A 234 MET cc_start: 0.7474 (mtm) cc_final: 0.7100 (mpp) REVERT: A 284 ARG cc_start: 0.7040 (ttm-80) cc_final: 0.6267 (ttm-80) REVERT: A 324 MET cc_start: 0.6611 (mmm) cc_final: 0.5298 (mmm) REVERT: A 356 CYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8381 (t) REVERT: A 471 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7021 (tt) outliers start: 16 outliers final: 11 residues processed: 81 average time/residue: 0.1317 time to fit residues: 13.9709 Evaluate side-chains 77 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 471 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 11 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.264086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.216254 restraints weight = 4840.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.223376 restraints weight = 2643.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.228346 restraints weight = 1731.723| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4099 Z= 0.186 Angle : 0.642 10.567 5601 Z= 0.310 Chirality : 0.038 0.117 661 Planarity : 0.005 0.053 697 Dihedral : 4.140 14.202 561 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.11 % Allowed : 23.19 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.38), residues: 526 helix: 1.92 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.07 (0.55), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 278 HIS 0.001 0.000 HIS A 47 PHE 0.011 0.001 PHE A 358 TYR 0.019 0.002 TYR A 180 ARG 0.003 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 90 ARG cc_start: 0.5641 (ttt180) cc_final: 0.5156 (ttt90) REVERT: A 95 GLN cc_start: 0.7716 (tp-100) cc_final: 0.7394 (tp40) REVERT: A 134 LYS cc_start: 0.7418 (tttt) cc_final: 0.7144 (ttpt) REVERT: A 147 MET cc_start: 0.6378 (mtt) cc_final: 0.5982 (tpp) REVERT: A 234 MET cc_start: 0.7457 (mtm) cc_final: 0.7063 (mpp) REVERT: A 284 ARG cc_start: 0.6964 (ttm-80) cc_final: 0.6182 (ttm-80) REVERT: A 324 MET cc_start: 0.6707 (mmm) cc_final: 0.6363 (mmm) REVERT: A 356 CYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8471 (t) REVERT: A 453 THR cc_start: 0.7010 (OUTLIER) cc_final: 0.5450 (p) REVERT: A 466 MET cc_start: 0.6054 (mmp) cc_final: 0.5678 (mmp) REVERT: A 471 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7030 (tt) outliers start: 17 outliers final: 10 residues processed: 77 average time/residue: 0.1397 time to fit residues: 14.0879 Evaluate side-chains 78 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 471 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS A 60 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.238259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.190375 restraints weight = 4802.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.196536 restraints weight = 2746.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.200815 restraints weight = 1870.642| |-----------------------------------------------------------------------------| r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4099 Z= 0.252 Angle : 0.700 9.424 5601 Z= 0.345 Chirality : 0.041 0.122 661 Planarity : 0.005 0.058 697 Dihedral : 4.294 17.074 561 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.86 % Allowed : 23.67 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.37), residues: 526 helix: 1.65 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.19 (0.55), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 357 HIS 0.003 0.001 HIS A 47 PHE 0.013 0.002 PHE A 358 TYR 0.016 0.002 TYR A 275 ARG 0.003 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6082 (pp30) REVERT: A 95 GLN cc_start: 0.7801 (tp-100) cc_final: 0.7476 (tp40) REVERT: A 147 MET cc_start: 0.6609 (mtt) cc_final: 0.6368 (tpp) REVERT: A 234 MET cc_start: 0.7674 (mtm) cc_final: 0.7315 (mpp) REVERT: A 284 ARG cc_start: 0.6971 (ttm-80) cc_final: 0.6296 (ttm-80) REVERT: A 324 MET cc_start: 0.7090 (mmm) cc_final: 0.6775 (mmm) REVERT: A 356 CYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8525 (t) REVERT: A 466 MET cc_start: 0.6485 (mmp) cc_final: 0.6087 (mmp) REVERT: A 471 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7355 (tt) outliers start: 16 outliers final: 7 residues processed: 85 average time/residue: 0.1505 time to fit residues: 16.6800 Evaluate side-chains 74 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 471 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 0.0070 chunk 30 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.0170 chunk 44 optimal weight: 3.9990 chunk 13 optimal weight: 0.0270 chunk 37 optimal weight: 0.8980 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 182 GLN ** A 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.248209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.198276 restraints weight = 4690.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.205231 restraints weight = 2644.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.209925 restraints weight = 1767.508| |-----------------------------------------------------------------------------| r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4099 Z= 0.191 Angle : 0.680 11.265 5601 Z= 0.329 Chirality : 0.039 0.144 661 Planarity : 0.005 0.053 697 Dihedral : 4.293 13.993 561 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.90 % Allowed : 25.85 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.38), residues: 526 helix: 1.84 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.21 (0.55), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.002 0.000 HIS A 47 PHE 0.014 0.001 PHE A 269 TYR 0.013 0.002 TYR A 180 ARG 0.005 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 60 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7313 (mp10) REVERT: A 90 ARG cc_start: 0.5733 (ttt180) cc_final: 0.5171 (ttt90) REVERT: A 95 GLN cc_start: 0.7758 (tp-100) cc_final: 0.7446 (tp40) REVERT: A 147 MET cc_start: 0.6482 (mtt) cc_final: 0.6268 (tpp) REVERT: A 222 MET cc_start: 0.6913 (tpp) cc_final: 0.5941 (tpp) REVERT: A 284 ARG cc_start: 0.7036 (ttm-80) cc_final: 0.6154 (ttm-80) REVERT: A 324 MET cc_start: 0.7041 (mmm) cc_final: 0.6736 (mmm) REVERT: A 356 CYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8457 (t) REVERT: A 471 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7106 (tt) outliers start: 12 outliers final: 6 residues processed: 77 average time/residue: 0.1307 time to fit residues: 13.2953 Evaluate side-chains 75 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 60 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 471 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 6.9990 chunk 28 optimal weight: 0.0270 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 0.0040 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 overall best weight: 0.3650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN ** A 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.248592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.203353 restraints weight = 4957.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.209594 restraints weight = 2832.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.213992 restraints weight = 1908.102| |-----------------------------------------------------------------------------| r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4099 Z= 0.191 Angle : 0.702 10.962 5601 Z= 0.337 Chirality : 0.040 0.133 661 Planarity : 0.005 0.052 697 Dihedral : 4.267 13.611 561 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.66 % Allowed : 26.09 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.38), residues: 526 helix: 1.87 (0.26), residues: 406 sheet: None (None), residues: 0 loop : -1.19 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.001 0.000 HIS A 47 PHE 0.037 0.002 PHE A 348 TYR 0.013 0.002 TYR A 275 ARG 0.003 0.000 ARG A 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1052 Ramachandran restraints generated. 526 Oldfield, 0 Emsley, 526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.5790 (ttt180) cc_final: 0.5250 (ttt90) REVERT: A 95 GLN cc_start: 0.7687 (tp-100) cc_final: 0.7345 (tp40) REVERT: A 147 MET cc_start: 0.6364 (mtt) cc_final: 0.6163 (tpp) REVERT: A 284 ARG cc_start: 0.7012 (ttm-80) cc_final: 0.6129 (ttm-80) REVERT: A 324 MET cc_start: 0.7037 (mmm) cc_final: 0.6726 (mmm) REVERT: A 356 CYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8392 (t) REVERT: A 471 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7099 (tt) outliers start: 11 outliers final: 8 residues processed: 76 average time/residue: 0.1277 time to fit residues: 12.8165 Evaluate side-chains 77 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.2978 > 50: distance: 65 - 69: 30.241 distance: 69 - 70: 13.864 distance: 70 - 71: 25.573 distance: 70 - 73: 13.571 distance: 71 - 72: 26.000 distance: 73 - 74: 4.845 distance: 73 - 75: 11.407 distance: 76 - 77: 18.157 distance: 77 - 78: 11.121 distance: 77 - 80: 12.953 distance: 78 - 79: 28.049 distance: 78 - 85: 12.604 distance: 80 - 81: 14.464 distance: 81 - 82: 19.982 distance: 82 - 83: 13.947 distance: 82 - 84: 18.407 distance: 85 - 86: 55.059 distance: 86 - 87: 17.825 distance: 86 - 89: 20.116 distance: 87 - 88: 41.072 distance: 87 - 91: 11.633 distance: 89 - 90: 26.804 distance: 92 - 93: 9.099 distance: 92 - 95: 27.731 distance: 93 - 94: 8.062 distance: 93 - 99: 25.401 distance: 95 - 96: 13.559 distance: 96 - 97: 10.236 distance: 96 - 98: 24.241 distance: 99 - 100: 23.084 distance: 99 - 105: 28.769 distance: 100 - 101: 8.187 distance: 100 - 103: 18.235 distance: 101 - 102: 15.209 distance: 101 - 106: 13.816 distance: 103 - 104: 33.848 distance: 104 - 105: 38.259 distance: 106 - 107: 13.165 distance: 107 - 108: 6.256 distance: 107 - 110: 34.097 distance: 108 - 109: 25.790 distance: 108 - 114: 6.945 distance: 110 - 111: 6.648 distance: 111 - 112: 14.066 distance: 111 - 113: 17.249 distance: 114 - 115: 9.770 distance: 114 - 120: 7.972 distance: 115 - 116: 16.965 distance: 115 - 118: 23.807 distance: 116 - 117: 20.631 distance: 116 - 121: 25.152 distance: 118 - 119: 22.169 distance: 119 - 120: 24.707 distance: 121 - 122: 17.797 distance: 122 - 123: 7.151 distance: 123 - 124: 17.713 distance: 123 - 129: 11.123 distance: 125 - 126: 13.172 distance: 126 - 127: 13.256 distance: 126 - 128: 10.872 distance: 129 - 130: 6.142 distance: 130 - 131: 9.569 distance: 130 - 133: 8.051 distance: 131 - 132: 9.132 distance: 131 - 136: 7.865 distance: 133 - 134: 20.615 distance: 133 - 135: 17.479 distance: 136 - 137: 6.923 distance: 137 - 138: 16.002 distance: 137 - 140: 8.687 distance: 138 - 139: 6.643 distance: 138 - 144: 15.589 distance: 140 - 141: 15.606 distance: 140 - 142: 20.166 distance: 141 - 143: 20.157