Starting phenix.real_space_refine on Fri Dec 27 09:40:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wjq_37589/12_2024/8wjq_37589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wjq_37589/12_2024/8wjq_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_37589/12_2024/8wjq_37589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wjq_37589/12_2024/8wjq_37589.map" model { file = "/net/cci-nas-00/data/ceres_data/8wjq_37589/12_2024/8wjq_37589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wjq_37589/12_2024/8wjq_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-5532/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: 2.97, per 1000 atoms: 0.74 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: 1.04 Conformation dependent library (CDL) restraints added in 526.8 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: 0.39 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: 1.11 Time building geometry restraints manager: 1.22 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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.940 Find NCS groups from input model: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- 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 : 0.395 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: 0.1399 time to fit residues: 13.3663 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 : 0.397 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 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 : 0.414 Fit side-chains outliers start: 13 outliers final: 5 residues processed: 86 average time/residue: 0.1172 time to fit residues: 13.5714 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 : 0.447 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4099 Z= 0.220 Angle : 0.680 11.440 5601 Z= 0.338 Chirality : 0.040 0.160 661 Planarity : 0.006 0.065 697 Dihedral : 4.269 15.182 561 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.66 % Allowed : 19.08 % Favored : 78.26 % 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: 1.69 (0.37), residues: 526 helix: 1.57 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -0.39 (0.58), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 357 HIS 0.005 0.001 HIS A 86 PHE 0.034 0.002 PHE A 269 TYR 0.017 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 78 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 95 GLN cc_start: 0.7361 (tp40) cc_final: 0.6900 (tp-100) REVERT: A 284 ARG cc_start: 0.7118 (ttm-80) cc_final: 0.6423 (ttm-80) outliers start: 11 outliers final: 7 residues processed: 76 average time/residue: 0.1571 time to fit residues: 15.2328 Evaluate side-chains 72 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 47 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN A 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4099 Z= 0.243 Angle : 0.690 11.368 5601 Z= 0.345 Chirality : 0.041 0.129 661 Planarity : 0.006 0.059 697 Dihedral : 4.321 18.455 561 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.38 % Allowed : 22.22 % Favored : 74.40 % 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: 1.46 (0.37), residues: 526 helix: 1.50 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -0.81 (0.56), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 357 HIS 0.005 0.001 HIS A 86 PHE 0.026 0.002 PHE A 269 TYR 0.015 0.002 TYR A 275 ARG 0.004 0.001 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 86 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 95 GLN cc_start: 0.7780 (tp-100) cc_final: 0.7347 (tp40) REVERT: A 284 ARG cc_start: 0.7073 (ttm-80) cc_final: 0.6324 (ttm-80) REVERT: A 324 MET cc_start: 0.6833 (mmm) cc_final: 0.6467 (mmm) REVERT: A 394 MET cc_start: 0.5841 (mmt) cc_final: 0.5564 (mmp) outliers start: 14 outliers final: 8 residues processed: 82 average time/residue: 0.1428 time to fit residues: 15.2726 Evaluate side-chains 74 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS A 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.3007 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= 0.200 Angle : 0.652 11.259 5601 Z= 0.318 Chirality : 0.039 0.121 661 Planarity : 0.005 0.055 697 Dihedral : 4.318 16.982 561 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.62 % Allowed : 23.19 % Favored : 73.19 % 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: 1.71 (0.37), residues: 526 helix: 1.70 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -0.81 (0.55), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 120 HIS 0.002 0.000 HIS A 47 PHE 0.014 0.001 PHE A 358 TYR 0.013 0.002 TYR A 275 ARG 0.002 0.000 ARG A 230 *********************** 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 82 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 90 ARG cc_start: 0.5528 (ttt180) cc_final: 0.4577 (ttm170) REVERT: A 95 GLN cc_start: 0.7765 (tp-100) cc_final: 0.7508 (tp40) REVERT: A 134 LYS cc_start: 0.7422 (tttt) cc_final: 0.7129 (ttpt) REVERT: A 147 MET cc_start: 0.6416 (mtt) cc_final: 0.6014 (tpp) REVERT: A 177 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7106 (m) REVERT: A 234 MET cc_start: 0.7638 (mtm) cc_final: 0.7429 (mmm) REVERT: A 284 ARG cc_start: 0.6954 (ttm-80) cc_final: 0.6165 (ttm-80) REVERT: A 356 CYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8359 (t) REVERT: A 394 MET cc_start: 0.5786 (mmt) cc_final: 0.5501 (mmp) outliers start: 15 outliers final: 11 residues processed: 80 average time/residue: 0.1479 time to fit residues: 15.4850 Evaluate side-chains 74 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET 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 354 THR 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 523 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 30.0000 chunk 30 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 0.0770 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.3150 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= 0.189 Angle : 0.645 10.736 5601 Z= 0.311 Chirality : 0.039 0.122 661 Planarity : 0.005 0.051 697 Dihedral : 4.264 16.217 561 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.35 % Allowed : 22.71 % Favored : 72.95 % 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: 1.77 (0.37), residues: 526 helix: 1.79 (0.26), residues: 409 sheet: None (None), residues: 0 loop : -1.00 (0.54), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 120 HIS 0.001 0.000 HIS A 47 PHE 0.012 0.001 PHE A 358 TYR 0.018 0.002 TYR A 180 ARG 0.003 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 84 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.5759 (ttt180) cc_final: 0.5335 (ttt90) REVERT: A 95 GLN cc_start: 0.7774 (tp-100) cc_final: 0.7456 (tp40) REVERT: A 120 TRP cc_start: 0.8055 (m100) cc_final: 0.7706 (m100) REVERT: A 147 MET cc_start: 0.6429 (mtt) cc_final: 0.6106 (tpp) REVERT: A 177 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7248 (m) REVERT: A 284 ARG cc_start: 0.6828 (ttm-80) cc_final: 0.6075 (ttm-80) REVERT: A 356 CYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8430 (t) REVERT: A 394 MET cc_start: 0.5683 (mmt) cc_final: 0.5308 (mmm) outliers start: 18 outliers final: 14 residues processed: 80 average time/residue: 0.1448 time to fit residues: 14.8451 Evaluate side-chains 76 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 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 293 ASP Chi-restraints excluded: chain A residue 354 THR 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 523 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 0.0070 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.3304 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= 0.187 Angle : 0.643 10.335 5601 Z= 0.310 Chirality : 0.038 0.122 661 Planarity : 0.005 0.050 697 Dihedral : 4.212 15.765 561 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.62 % Allowed : 24.64 % Favored : 71.74 % 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: 1.83 (0.37), residues: 526 helix: 1.90 (0.26), residues: 407 sheet: None (None), residues: 0 loop : -1.22 (0.54), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 120 HIS 0.001 0.000 HIS A 47 PHE 0.012 0.001 PHE A 358 TYR 0.014 0.002 TYR A 275 ARG 0.002 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 81 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ARG cc_start: 0.5635 (ttt180) cc_final: 0.5259 (ttt90) REVERT: A 95 GLN cc_start: 0.7754 (tp-100) cc_final: 0.7433 (tp40) REVERT: A 120 TRP cc_start: 0.8129 (m100) cc_final: 0.7851 (m100) REVERT: A 147 MET cc_start: 0.6428 (mtt) cc_final: 0.6188 (tpp) REVERT: A 284 ARG cc_start: 0.6847 (ttm-80) cc_final: 0.6261 (ttm-80) REVERT: A 324 MET cc_start: 0.6576 (mmm) cc_final: 0.6251 (mmm) REVERT: A 356 CYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8506 (t) REVERT: A 394 MET cc_start: 0.5678 (mmt) cc_final: 0.5326 (mmm) REVERT: A 466 MET cc_start: 0.6149 (mmp) cc_final: 0.5745 (mmp) outliers start: 15 outliers final: 13 residues processed: 78 average time/residue: 0.1311 time to fit residues: 13.5173 Evaluate side-chains 76 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 188 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 277 TRP Chi-restraints excluded: chain A residue 354 THR 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 488 LEU Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 0.2980 chunk 4 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4099 Z= 0.194 Angle : 0.655 9.574 5601 Z= 0.313 Chirality : 0.039 0.135 661 Planarity : 0.005 0.050 697 Dihedral : 4.218 15.506 561 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.62 % Allowed : 25.85 % Favored : 70.53 % 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: 1.72 (0.37), residues: 526 helix: 1.81 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.26 (0.54), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.001 0.000 HIS A 245 PHE 0.012 0.001 PHE A 358 TYR 0.014 0.002 TYR A 275 ARG 0.001 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 78 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.428 Fit side-chains REVERT: A 90 ARG cc_start: 0.5730 (ttt180) cc_final: 0.5440 (ttt90) REVERT: A 95 GLN cc_start: 0.7773 (tp-100) cc_final: 0.7436 (tp40) REVERT: A 120 TRP cc_start: 0.8136 (m100) cc_final: 0.7854 (m100) REVERT: A 147 MET cc_start: 0.6443 (mtt) cc_final: 0.6224 (tpp) REVERT: A 284 ARG cc_start: 0.6786 (ttm-80) cc_final: 0.6147 (ttm-80) REVERT: A 356 CYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8506 (t) REVERT: A 394 MET cc_start: 0.6103 (OUTLIER) cc_final: 0.5749 (mmm) outliers start: 15 outliers final: 10 residues processed: 75 average time/residue: 0.1360 time to fit residues: 13.3374 Evaluate side-chains 74 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 277 TRP Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4099 Z= 0.204 Angle : 0.691 9.813 5601 Z= 0.329 Chirality : 0.040 0.167 661 Planarity : 0.005 0.054 697 Dihedral : 4.241 14.968 561 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.35 % Allowed : 25.12 % Favored : 70.53 % 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: 1.59 (0.37), residues: 526 helix: 1.73 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.36 (0.54), residues: 118 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 0.012 0.001 PHE A 358 TYR 0.014 0.002 TYR A 275 ARG 0.001 0.000 ARG A 284 *********************** 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 86 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 90 ARG cc_start: 0.5661 (ttt180) cc_final: 0.5408 (ttt90) REVERT: A 95 GLN cc_start: 0.7772 (tp-100) cc_final: 0.7461 (tp40) REVERT: A 120 TRP cc_start: 0.8130 (m100) cc_final: 0.7859 (m100) REVERT: A 130 THR cc_start: 0.8510 (t) cc_final: 0.8231 (p) REVERT: A 147 MET cc_start: 0.6541 (mtt) cc_final: 0.6332 (tpp) REVERT: A 234 MET cc_start: 0.7487 (mmm) cc_final: 0.6263 (mmm) REVERT: A 284 ARG cc_start: 0.6786 (ttm-80) cc_final: 0.6172 (ttm-80) REVERT: A 356 CYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8518 (t) REVERT: A 394 MET cc_start: 0.6195 (OUTLIER) cc_final: 0.5826 (mmm) outliers start: 18 outliers final: 12 residues processed: 82 average time/residue: 0.1205 time to fit residues: 13.0448 Evaluate side-chains 81 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 5.9990 chunk 48 optimal weight: 0.0870 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 9.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4099 Z= 0.198 Angle : 0.703 9.554 5601 Z= 0.340 Chirality : 0.040 0.145 661 Planarity : 0.005 0.053 697 Dihedral : 4.227 14.874 561 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.38 % Allowed : 25.36 % 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: 1.59 (0.37), residues: 526 helix: 1.74 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.41 (0.54), 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 0.037 0.002 PHE A 348 TYR 0.013 0.002 TYR A 275 ARG 0.002 0.000 ARG A 347 ********************** 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 81 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 50 TRP cc_start: 0.7318 (t60) cc_final: 0.7001 (t60) REVERT: A 95 GLN cc_start: 0.7759 (tp-100) cc_final: 0.7382 (tp40) REVERT: A 120 TRP cc_start: 0.8071 (m100) cc_final: 0.7813 (m100) REVERT: A 147 MET cc_start: 0.6526 (mtt) cc_final: 0.6316 (tpp) REVERT: A 186 MET cc_start: 0.5306 (mmt) cc_final: 0.5085 (mmm) REVERT: A 284 ARG cc_start: 0.6828 (ttm-80) cc_final: 0.6051 (ttm-80) REVERT: A 324 MET cc_start: 0.6649 (mmm) cc_final: 0.6269 (mmm) REVERT: A 356 CYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8472 (t) REVERT: A 394 MET cc_start: 0.6230 (OUTLIER) cc_final: 0.5865 (mmm) outliers start: 14 outliers final: 12 residues processed: 77 average time/residue: 0.1360 time to fit residues: 14.0081 Evaluate side-chains 81 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 394 MET Chi-restraints excluded: chain A residue 402 HIS Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 523 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 5.9990 chunk 42 optimal weight: 0.0010 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.0870 chunk 36 optimal weight: 0.0870 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 28 optimal weight: 0.0170 overall best weight: 0.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.273727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.228042 restraints weight = 4860.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.235362 restraints weight = 2590.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.240025 restraints weight = 1647.733| |-----------------------------------------------------------------------------| r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5987 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4099 Z= 0.174 Angle : 0.690 8.917 5601 Z= 0.329 Chirality : 0.039 0.155 661 Planarity : 0.005 0.048 697 Dihedral : 4.181 13.768 561 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.38 % Allowed : 24.88 % Favored : 71.74 % 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 (0.38), residues: 526 helix: 1.85 (0.26), residues: 408 sheet: None (None), residues: 0 loop : -1.23 (0.56), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.001 0.000 HIS A 86 PHE 0.040 0.002 PHE A 348 TYR 0.013 0.002 TYR A 275 ARG 0.002 0.000 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1097.12 seconds wall clock time: 20 minutes 48.89 seconds (1248.89 seconds total)