Starting phenix.real_space_refine on Fri Dec 27 11:47:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pdd_13334/12_2024/7pdd_13334.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pdd_13334/12_2024/7pdd_13334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pdd_13334/12_2024/7pdd_13334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pdd_13334/12_2024/7pdd_13334.map" model { file = "/net/cci-nas-00/data/ceres_data/7pdd_13334/12_2024/7pdd_13334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pdd_13334/12_2024/7pdd_13334.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 33 5.16 5 C 2847 2.51 5 N 772 2.21 5 O 864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 4516 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3550 Classifications: {'peptide': 449} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 439} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Time building chain proxies: 3.44, per 1000 atoms: 0.76 Number of scatterers: 4516 At special positions: 0 Unit cell: (94.77, 77.76, 79.38, 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 33 16.00 O 864 8.00 N 772 7.00 C 2847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.14 Conformation dependent library (CDL) restraints added in 549.9 milliseconds 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1058 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 4 sheets defined 50.1% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 321 through 335 Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.552A pdb=" N LYS A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 removed outlier: 3.694A pdb=" N GLU A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.602A pdb=" N MET A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 434 Processing helix chain 'A' and resid 457 through 481 Processing helix chain 'A' and resid 511 through 523 removed outlier: 3.779A pdb=" N ASN A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 1021 through 1037 Processing helix chain 'A' and resid 1038 through 1047 Processing helix chain 'A' and resid 1067 through 1072 removed outlier: 3.699A pdb=" N PHE A1071 " --> pdb=" O ASN A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1097 removed outlier: 3.912A pdb=" N LEU A1097 " --> pdb=" O PHE A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1157 removed outlier: 3.878A pdb=" N GLN A1137 " --> pdb=" O GLN A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1200 removed outlier: 4.280A pdb=" N ASN A1193 " --> pdb=" O GLY A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1219 removed outlier: 3.625A pdb=" N LYS A1219 " --> pdb=" O ARG A1215 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 25 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 92 through 102 Processing helix chain 'B' and resid 115 through 123 Processing helix chain 'B' and resid 125 through 134 Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 439 removed outlier: 7.373A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 394 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLN A 389 " --> pdb=" O CYS A 497 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS A 497 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLU A 391 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 495 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439 removed outlier: 7.373A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 394 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLN A 389 " --> pdb=" O CYS A 497 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N CYS A 497 " --> pdb=" O GLN A 389 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLU A 391 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 495 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A 532 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A 492 " --> pdb=" O SER A 532 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1052 through 1055 Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1109 removed outlier: 7.182A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N GLN A1208 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A1166 " --> pdb=" O GLN A1208 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A1241 " --> pdb=" O VAL A1209 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A1228 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A1242 " --> pdb=" O TYR A1226 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR A1226 " --> pdb=" O LEU A1242 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 756 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: 1.40 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1515 1.34 - 1.46: 976 1.46 - 1.58: 2050 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 4595 Sorted by residual: bond pdb=" N ASP A 541 " pdb=" CA ASP A 541 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.69e+00 bond pdb=" N GLU A 453 " pdb=" CA GLU A 453 " ideal model delta sigma weight residual 1.460 1.446 0.014 1.29e-02 6.01e+03 1.11e+00 bond pdb=" CA ASN A1035 " pdb=" C ASN A1035 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.24e-02 6.50e+03 8.21e-01 bond pdb=" C GLU A 453 " pdb=" O GLU A 453 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.75e-01 bond pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.66e-01 ... (remaining 4590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 5935 1.58 - 3.15: 212 3.15 - 4.73: 33 4.73 - 6.30: 6 6.30 - 7.88: 3 Bond angle restraints: 6189 Sorted by residual: angle pdb=" N TYR A 446 " pdb=" CA TYR A 446 " pdb=" C TYR A 446 " ideal model delta sigma weight residual 108.79 113.27 -4.48 1.53e+00 4.27e-01 8.58e+00 angle pdb=" C TYR A 445 " pdb=" N TYR A 446 " pdb=" CA TYR A 446 " ideal model delta sigma weight residual 121.62 116.31 5.31 1.83e+00 2.99e-01 8.43e+00 angle pdb=" C LYS A 437 " pdb=" N ILE A 438 " pdb=" CA ILE A 438 " ideal model delta sigma weight residual 121.97 117.45 4.52 1.80e+00 3.09e-01 6.29e+00 angle pdb=" N ASN A 409 " pdb=" CA ASN A 409 " pdb=" C ASN A 409 " ideal model delta sigma weight residual 110.44 113.29 -2.85 1.20e+00 6.94e-01 5.63e+00 angle pdb=" C THR A1181 " pdb=" N LYS A1182 " pdb=" CA LYS A1182 " ideal model delta sigma weight residual 122.39 126.25 -3.86 1.64e+00 3.72e-01 5.54e+00 ... (remaining 6184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 2448 17.24 - 34.48: 248 34.48 - 51.72: 44 51.72 - 68.96: 7 68.96 - 86.20: 5 Dihedral angle restraints: 2752 sinusoidal: 1102 harmonic: 1650 Sorted by residual: dihedral pdb=" CA THR A1180 " pdb=" C THR A1180 " pdb=" N THR A1181 " pdb=" CA THR A1181 " ideal model delta harmonic sigma weight residual -180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA TYR A1072 " pdb=" C TYR A1072 " pdb=" N GLU A1073 " pdb=" CA GLU A1073 " ideal model delta harmonic sigma weight residual 180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA LYS A 321 " pdb=" C LYS A 321 " pdb=" N ASP A 322 " pdb=" CA ASP A 322 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 2749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 383 0.029 - 0.059: 186 0.059 - 0.088: 78 0.088 - 0.117: 29 0.117 - 0.146: 4 Chirality restraints: 680 Sorted by residual: chirality pdb=" CA ASP A 541 " pdb=" N ASP A 541 " pdb=" C ASP A 541 " pdb=" CB ASP A 541 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE A 395 " pdb=" N ILE A 395 " pdb=" C ILE A 395 " pdb=" CB ILE A 395 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA VAL A 509 " pdb=" N VAL A 509 " pdb=" C VAL A 509 " pdb=" CB VAL A 509 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 677 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1037 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO A1038 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1072 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C TYR A1072 " -0.023 2.00e-02 2.50e+03 pdb=" O TYR A1072 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU A1073 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 453 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO A 454 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 454 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 454 " 0.017 5.00e-02 4.00e+02 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 95 2.65 - 3.22: 4861 3.22 - 3.78: 7361 3.78 - 4.34: 9956 4.34 - 4.90: 15254 Nonbonded interactions: 37527 Sorted by model distance: nonbonded pdb=" O SER A 532 " pdb=" OG1 THR A 535 " model vdw 2.092 3.040 nonbonded pdb=" O ALA A 412 " pdb=" OG SER A1052 " model vdw 2.093 3.040 nonbonded pdb=" OH TYR A1226 " pdb=" OG1 THR A1229 " model vdw 2.153 3.040 nonbonded pdb=" O SER A1196 " pdb=" OG1 THR A1200 " model vdw 2.218 3.040 nonbonded pdb=" NH2 ARG A1206 " pdb=" O PRO A1244 " model vdw 2.222 3.120 ... (remaining 37522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.130 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.004 0.044 4595 Z= 0.254 Angle : 0.748 7.879 6189 Z= 0.445 Chirality : 0.042 0.146 680 Planarity : 0.004 0.048 803 Dihedral : 14.377 86.204 1694 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.29), residues: 567 helix: -2.34 (0.25), residues: 273 sheet: -2.54 (0.40), residues: 105 loop : -3.08 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1031 HIS 0.005 0.002 HIS A1170 PHE 0.010 0.002 PHE A1224 TYR 0.015 0.002 TYR A1241 ARG 0.003 0.000 ARG A1165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8592 (m-10) cc_final: 0.8227 (m-80) REVERT: A 425 ARG cc_start: 0.8923 (mtt180) cc_final: 0.8453 (mtp180) REVERT: A 429 LEU cc_start: 0.9525 (tp) cc_final: 0.9280 (tt) REVERT: B 56 TRP cc_start: 0.7689 (t60) cc_final: 0.7441 (t-100) REVERT: B 114 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8269 (mmtt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2561 time to fit residues: 42.0459 Evaluate side-chains 101 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 0.0670 chunk 32 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 HIS A1154 ASN A1237 GLN B 92 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4595 Z= 0.200 Angle : 0.677 7.255 6189 Z= 0.360 Chirality : 0.044 0.152 680 Planarity : 0.004 0.056 803 Dihedral : 5.238 24.604 615 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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: -2.47 (0.31), residues: 567 helix: -0.82 (0.28), residues: 280 sheet: -2.08 (0.43), residues: 105 loop : -2.40 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1159 HIS 0.004 0.001 HIS B 92 PHE 0.013 0.002 PHE A1168 TYR 0.019 0.002 TYR A 446 ARG 0.005 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8430 (m-10) cc_final: 0.8105 (m-80) REVERT: A 425 ARG cc_start: 0.8842 (mtt180) cc_final: 0.8027 (mtp180) REVERT: A 510 TRP cc_start: 0.7017 (m-90) cc_final: 0.6808 (m-90) REVERT: A 520 MET cc_start: 0.7202 (ttm) cc_final: 0.6931 (mtp) REVERT: A 543 TYR cc_start: 0.7133 (m-80) cc_final: 0.6606 (m-80) REVERT: A 1075 ASN cc_start: 0.7774 (m-40) cc_final: 0.7495 (p0) REVERT: A 1081 GLU cc_start: 0.7613 (tp30) cc_final: 0.7381 (tp30) REVERT: A 1084 ARG cc_start: 0.8784 (mtt90) cc_final: 0.8042 (mtt-85) REVERT: A 1141 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8408 (mm-30) REVERT: A 1146 MET cc_start: 0.8841 (ppp) cc_final: 0.8575 (ppp) REVERT: B 56 TRP cc_start: 0.7639 (t60) cc_final: 0.7431 (t-100) REVERT: B 112 PHE cc_start: 0.7262 (m-80) cc_final: 0.7046 (m-80) REVERT: B 114 LYS cc_start: 0.8358 (mmtt) cc_final: 0.7976 (mmtt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1905 time to fit residues: 32.1413 Evaluate side-chains 106 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4595 Z= 0.256 Angle : 0.681 8.246 6189 Z= 0.365 Chirality : 0.043 0.145 680 Planarity : 0.004 0.057 803 Dihedral : 5.280 24.632 615 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % 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: -2.00 (0.32), residues: 567 helix: -0.42 (0.28), residues: 281 sheet: -1.72 (0.46), residues: 99 loop : -2.32 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A1159 HIS 0.006 0.001 HIS A1170 PHE 0.011 0.002 PHE A1168 TYR 0.019 0.002 TYR A 446 ARG 0.002 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8547 (m-10) cc_final: 0.8175 (m-80) REVERT: A 465 MET cc_start: 0.8244 (tmm) cc_final: 0.7776 (tmm) REVERT: A 1075 ASN cc_start: 0.7800 (m-40) cc_final: 0.7434 (p0) REVERT: A 1084 ARG cc_start: 0.8747 (mtt90) cc_final: 0.8082 (mtt-85) REVERT: A 1146 MET cc_start: 0.8863 (ppp) cc_final: 0.8561 (ppp) REVERT: A 1198 MET cc_start: 0.8422 (mtp) cc_final: 0.8190 (tmm) REVERT: B 16 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8691 (mmtm) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1948 time to fit residues: 29.1243 Evaluate side-chains 95 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4595 Z= 0.189 Angle : 0.653 6.874 6189 Z= 0.348 Chirality : 0.043 0.148 680 Planarity : 0.004 0.055 803 Dihedral : 4.996 23.838 615 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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 (0.33), residues: 567 helix: -0.31 (0.28), residues: 284 sheet: -1.30 (0.49), residues: 99 loop : -2.15 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 56 HIS 0.006 0.001 HIS A 530 PHE 0.011 0.001 PHE A1168 TYR 0.020 0.002 TYR A 446 ARG 0.008 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8430 (m-10) cc_final: 0.7983 (m-80) REVERT: A 543 TYR cc_start: 0.6338 (m-80) cc_final: 0.5286 (m-80) REVERT: A 1075 ASN cc_start: 0.7770 (m-40) cc_final: 0.7551 (p0) REVERT: A 1141 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8511 (mm-30) REVERT: A 1146 MET cc_start: 0.8843 (ppp) cc_final: 0.8531 (ppp) REVERT: B 112 PHE cc_start: 0.7335 (m-80) cc_final: 0.7124 (m-80) REVERT: B 114 LYS cc_start: 0.8365 (mmtt) cc_final: 0.8062 (mmtt) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2037 time to fit residues: 30.7629 Evaluate side-chains 92 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4595 Z= 0.229 Angle : 0.691 8.538 6189 Z= 0.367 Chirality : 0.044 0.147 680 Planarity : 0.004 0.051 803 Dihedral : 5.094 23.960 615 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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 (0.33), residues: 567 helix: -0.37 (0.28), residues: 283 sheet: -1.15 (0.49), residues: 99 loop : -2.17 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP B 56 HIS 0.004 0.001 HIS A 530 PHE 0.008 0.001 PHE A1093 TYR 0.022 0.002 TYR A 446 ARG 0.004 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8541 (m-10) cc_final: 0.8036 (m-80) REVERT: A 1084 ARG cc_start: 0.8785 (mtt90) cc_final: 0.8213 (mtt-85) REVERT: A 1141 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8448 (mm-30) REVERT: A 1198 MET cc_start: 0.8301 (ppp) cc_final: 0.7977 (ppp) REVERT: B 112 PHE cc_start: 0.7436 (m-80) cc_final: 0.7186 (m-80) REVERT: B 114 LYS cc_start: 0.8460 (mmtt) cc_final: 0.8141 (mmtt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1974 time to fit residues: 29.3996 Evaluate side-chains 95 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4595 Z= 0.200 Angle : 0.672 9.275 6189 Z= 0.355 Chirality : 0.044 0.143 680 Planarity : 0.004 0.050 803 Dihedral : 5.028 23.003 615 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.21 % Allowed : 2.08 % Favored : 97.71 % 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: -1.58 (0.34), residues: 567 helix: -0.27 (0.29), residues: 283 sheet: -1.01 (0.50), residues: 99 loop : -2.11 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP B 56 HIS 0.004 0.001 HIS B 59 PHE 0.010 0.001 PHE A1168 TYR 0.013 0.002 TYR A1083 ARG 0.007 0.001 ARG A1206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8498 (m-10) cc_final: 0.8001 (m-80) REVERT: A 1084 ARG cc_start: 0.8673 (mtt90) cc_final: 0.8194 (mtt-85) REVERT: A 1141 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8430 (mm-30) REVERT: A 1146 MET cc_start: 0.8831 (ppp) cc_final: 0.8482 (ppp) REVERT: B 14 LEU cc_start: 0.7299 (mt) cc_final: 0.6857 (mp) REVERT: B 112 PHE cc_start: 0.7388 (m-80) cc_final: 0.7167 (m-80) REVERT: B 114 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8173 (mmtt) outliers start: 1 outliers final: 0 residues processed: 123 average time/residue: 0.1848 time to fit residues: 28.1030 Evaluate side-chains 90 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4595 Z= 0.198 Angle : 0.714 10.418 6189 Z= 0.375 Chirality : 0.044 0.147 680 Planarity : 0.004 0.049 803 Dihedral : 4.922 23.100 615 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -1.62 (0.34), residues: 567 helix: -0.42 (0.29), residues: 284 sheet: -0.89 (0.51), residues: 99 loop : -2.02 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP B 56 HIS 0.005 0.001 HIS B 59 PHE 0.010 0.001 PHE A1168 TYR 0.012 0.002 TYR A1083 ARG 0.004 0.000 ARG A1206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8467 (m-10) cc_final: 0.7961 (m-80) REVERT: A 520 MET cc_start: 0.6128 (ttt) cc_final: 0.5583 (tmm) REVERT: A 1084 ARG cc_start: 0.8657 (mtt90) cc_final: 0.8024 (mtt-85) REVERT: A 1141 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8477 (mm-30) REVERT: A 1146 MET cc_start: 0.8847 (ppp) cc_final: 0.8476 (ppp) REVERT: B 23 ARG cc_start: 0.8745 (ptm160) cc_final: 0.8487 (ptm-80) REVERT: B 114 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8187 (mmtt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1997 time to fit residues: 28.2120 Evaluate side-chains 87 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.0020 chunk 5 optimal weight: 7.9990 chunk 42 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4595 Z= 0.192 Angle : 0.709 11.030 6189 Z= 0.374 Chirality : 0.045 0.172 680 Planarity : 0.004 0.047 803 Dihedral : 4.855 23.361 615 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -1.52 (0.34), residues: 567 helix: -0.36 (0.29), residues: 284 sheet: -0.83 (0.50), residues: 99 loop : -1.93 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP B 56 HIS 0.004 0.001 HIS B 59 PHE 0.016 0.001 PHE A1142 TYR 0.014 0.001 TYR A 446 ARG 0.007 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8434 (m-10) cc_final: 0.7958 (m-80) REVERT: A 520 MET cc_start: 0.6343 (ttt) cc_final: 0.5591 (tmm) REVERT: A 1084 ARG cc_start: 0.8681 (mtt90) cc_final: 0.8007 (mtt-85) REVERT: A 1141 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8561 (mm-30) REVERT: A 1146 MET cc_start: 0.8883 (ppp) cc_final: 0.8456 (ppp) REVERT: A 1238 MET cc_start: 0.8005 (mtm) cc_final: 0.7745 (mpp) REVERT: B 16 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8190 (mmtm) REVERT: B 114 LYS cc_start: 0.8470 (mmtt) cc_final: 0.8231 (mmtt) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1948 time to fit residues: 27.6809 Evaluate side-chains 94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4595 Z= 0.204 Angle : 0.723 11.199 6189 Z= 0.380 Chirality : 0.045 0.184 680 Planarity : 0.004 0.047 803 Dihedral : 4.866 22.727 615 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -1.47 (0.34), residues: 567 helix: -0.27 (0.29), residues: 285 sheet: -0.89 (0.50), residues: 101 loop : -1.95 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP B 56 HIS 0.005 0.001 HIS B 59 PHE 0.009 0.001 PHE A1168 TYR 0.014 0.001 TYR A 446 ARG 0.011 0.001 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8449 (m-10) cc_final: 0.7991 (m-80) REVERT: A 520 MET cc_start: 0.6266 (ttt) cc_final: 0.5420 (tmm) REVERT: A 569 TYR cc_start: 0.7801 (m-80) cc_final: 0.7486 (m-80) REVERT: A 1084 ARG cc_start: 0.8718 (mtt90) cc_final: 0.8007 (mtt-85) REVERT: A 1141 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8499 (mm-30) REVERT: A 1146 MET cc_start: 0.8870 (ppp) cc_final: 0.8551 (ppp) REVERT: A 1198 MET cc_start: 0.8161 (ppp) cc_final: 0.7742 (ppp) REVERT: A 1238 MET cc_start: 0.8104 (mtm) cc_final: 0.7747 (mpp) REVERT: B 16 LYS cc_start: 0.8747 (mmmt) cc_final: 0.8527 (mmtm) REVERT: B 114 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8278 (mmtt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1972 time to fit residues: 27.7965 Evaluate side-chains 89 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4595 Z= 0.203 Angle : 0.721 11.943 6189 Z= 0.380 Chirality : 0.045 0.171 680 Planarity : 0.004 0.055 803 Dihedral : 4.908 22.511 615 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -1.32 (0.34), residues: 567 helix: -0.18 (0.29), residues: 285 sheet: -0.50 (0.54), residues: 84 loop : -1.95 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 56 HIS 0.008 0.001 HIS A 530 PHE 0.010 0.001 PHE A1168 TYR 0.012 0.001 TYR A 446 ARG 0.009 0.001 ARG B 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 PHE cc_start: 0.8441 (m-10) cc_final: 0.7960 (m-80) REVERT: A 520 MET cc_start: 0.6261 (ttt) cc_final: 0.5461 (tmm) REVERT: A 569 TYR cc_start: 0.7708 (m-80) cc_final: 0.7435 (m-80) REVERT: A 1030 ASP cc_start: 0.8010 (t70) cc_final: 0.7648 (t0) REVERT: A 1084 ARG cc_start: 0.8740 (mtt90) cc_final: 0.7986 (mtt-85) REVERT: A 1141 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8456 (mm-30) REVERT: A 1146 MET cc_start: 0.8895 (ppp) cc_final: 0.8519 (ppp) REVERT: A 1198 MET cc_start: 0.8172 (ppp) cc_final: 0.7750 (ppp) REVERT: A 1238 MET cc_start: 0.8132 (mtm) cc_final: 0.7763 (mpp) REVERT: B 16 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8511 (mmtm) REVERT: B 30 VAL cc_start: 0.9046 (t) cc_final: 0.8829 (t) REVERT: B 114 LYS cc_start: 0.8518 (mmtt) cc_final: 0.8292 (mmtt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1882 time to fit residues: 27.4205 Evaluate side-chains 96 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.0030 chunk 50 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.099856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.078143 restraints weight = 17379.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.080127 restraints weight = 12213.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.081654 restraints weight = 9395.009| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4595 Z= 0.206 Angle : 0.735 11.972 6189 Z= 0.388 Chirality : 0.045 0.156 680 Planarity : 0.004 0.051 803 Dihedral : 4.965 25.380 615 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: -1.25 (0.34), residues: 567 helix: -0.10 (0.29), residues: 290 sheet: -0.14 (0.57), residues: 76 loop : -2.12 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 56 HIS 0.006 0.001 HIS A 530 PHE 0.009 0.001 PHE A1168 TYR 0.014 0.001 TYR A 446 ARG 0.011 0.001 ARG B 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1482.04 seconds wall clock time: 27 minutes 44.21 seconds (1664.21 seconds total)