Starting phenix.real_space_refine on Wed Jun 4 11:41:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9boj_44744/06_2025/9boj_44744.cif Found real_map, /net/cci-nas-00/data/ceres_data/9boj_44744/06_2025/9boj_44744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9boj_44744/06_2025/9boj_44744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9boj_44744/06_2025/9boj_44744.map" model { file = "/net/cci-nas-00/data/ceres_data/9boj_44744/06_2025/9boj_44744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9boj_44744/06_2025/9boj_44744.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.041 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 14 5.16 5 C 1728 2.51 5 N 401 2.21 5 O 417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 2560 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2560 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 4, 'TRANS': 316} Chain breaks: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 98 Time building chain proxies: 2.89, per 1000 atoms: 1.13 Number of scatterers: 2560 At special positions: 0 Unit cell: (73.425, 58.575, 75.9, 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 14 16.00 O 417 8.00 N 401 7.00 C 1728 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: 0.62 Conformation dependent library (CDL) restraints added in 292.7 milliseconds 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 618 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 84.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'B' and resid 111 through 131 removed outlier: 4.112A pdb=" N ILE B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 141 through 166 removed outlier: 3.836A pdb=" N VAL B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 283 removed outlier: 8.089A pdb=" N GLN B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 313 Processing helix chain 'B' and resid 313 through 328 Processing helix chain 'B' and resid 332 through 360 Processing helix chain 'B' and resid 368 through 419 removed outlier: 3.835A pdb=" N ILE B 374 " --> pdb=" O MET B 370 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 441 Processing helix chain 'B' and resid 453 through 478 Processing helix chain 'B' and resid 487 through 513 removed outlier: 3.638A pdb=" N ALA B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL B 495 " --> pdb=" O ALA B 491 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.64 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 747 1.34 - 1.46: 781 1.46 - 1.58: 1095 1.58 - 1.69: 0 1.69 - 1.81: 21 Bond restraints: 2644 Sorted by residual: bond pdb=" N TRP B 166 " pdb=" CA TRP B 166 " ideal model delta sigma weight residual 1.458 1.479 -0.021 1.90e-02 2.77e+03 1.18e+00 bond pdb=" N ASP B 363 " pdb=" CA ASP B 363 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.28e-01 bond pdb=" CA ASP B 363 " pdb=" CB ASP B 363 " ideal model delta sigma weight residual 1.530 1.516 0.014 1.69e-02 3.50e+03 7.11e-01 bond pdb=" CA ASP B 363 " pdb=" C ASP B 363 " ideal model delta sigma weight residual 1.523 1.531 -0.008 1.34e-02 5.57e+03 3.17e-01 bond pdb=" CB TRP B 378 " pdb=" CG TRP B 378 " ideal model delta sigma weight residual 1.498 1.515 -0.017 3.10e-02 1.04e+03 2.86e-01 ... (remaining 2639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 3552 1.60 - 3.20: 51 3.20 - 4.80: 10 4.80 - 6.40: 2 6.40 - 8.00: 2 Bond angle restraints: 3617 Sorted by residual: angle pdb=" CA TRP B 166 " pdb=" CB TRP B 166 " pdb=" CG TRP B 166 " ideal model delta sigma weight residual 113.60 121.60 -8.00 1.90e+00 2.77e-01 1.77e+01 angle pdb=" N TRP B 166 " pdb=" CA TRP B 166 " pdb=" CB TRP B 166 " ideal model delta sigma weight residual 110.50 116.89 -6.39 1.70e+00 3.46e-01 1.41e+01 angle pdb=" CA TRP B 378 " pdb=" CB TRP B 378 " pdb=" CG TRP B 378 " ideal model delta sigma weight residual 113.60 120.16 -6.56 1.90e+00 2.77e-01 1.19e+01 angle pdb=" CA TRP B 166 " pdb=" C TRP B 166 " pdb=" O TRP B 166 " ideal model delta sigma weight residual 120.80 116.98 3.82 1.70e+00 3.46e-01 5.06e+00 angle pdb=" C ASP B 363 " pdb=" CA ASP B 363 " pdb=" CB ASP B 363 " ideal model delta sigma weight residual 110.42 114.84 -4.42 1.99e+00 2.53e-01 4.93e+00 ... (remaining 3612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 1324 16.49 - 32.98: 92 32.98 - 49.47: 30 49.47 - 65.96: 7 65.96 - 82.45: 2 Dihedral angle restraints: 1455 sinusoidal: 504 harmonic: 951 Sorted by residual: dihedral pdb=" N GLN B 160 " pdb=" CA GLN B 160 " pdb=" CB GLN B 160 " pdb=" CG GLN B 160 " ideal model delta sinusoidal sigma weight residual -180.00 -120.18 -59.82 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N MET B 295 " pdb=" CA MET B 295 " pdb=" CB MET B 295 " pdb=" CG MET B 295 " ideal model delta sinusoidal sigma weight residual 180.00 120.68 59.32 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB GLU B 298 " pdb=" CG GLU B 298 " pdb=" CD GLU B 298 " pdb=" OE1 GLU B 298 " ideal model delta sinusoidal sigma weight residual 0.00 -82.45 82.45 1 3.00e+01 1.11e-03 9.26e+00 ... (remaining 1452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 254 0.028 - 0.056: 119 0.056 - 0.084: 31 0.084 - 0.112: 7 0.112 - 0.140: 1 Chirality restraints: 412 Sorted by residual: chirality pdb=" CA TRP B 166 " pdb=" N TRP B 166 " pdb=" C TRP B 166 " pdb=" CB TRP B 166 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CA ILE B 483 " pdb=" N ILE B 483 " pdb=" C ILE B 483 " pdb=" CB ILE B 483 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.03e-01 chirality pdb=" CA PHE B 311 " pdb=" N PHE B 311 " pdb=" C PHE B 311 " pdb=" CB PHE B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.64e-01 ... (remaining 409 not shown) Planarity restraints: 430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 165 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C ARG B 165 " 0.071 2.00e-02 2.50e+03 pdb=" O ARG B 165 " -0.026 2.00e-02 2.50e+03 pdb=" N TRP B 166 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 166 " 0.016 2.00e-02 2.50e+03 1.40e-02 4.93e+00 pdb=" CG TRP B 166 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP B 166 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 166 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 166 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 166 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 166 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 166 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 166 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 166 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 261 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C ILE B 261 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE B 261 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU B 262 " 0.012 2.00e-02 2.50e+03 ... (remaining 427 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 895 2.85 - 3.36: 2680 3.36 - 3.87: 4274 3.87 - 4.39: 4450 4.39 - 4.90: 8049 Nonbonded interactions: 20348 Sorted by model distance: nonbonded pdb=" O TYR B 441 " pdb=" OH TYR B 460 " model vdw 2.333 3.040 nonbonded pdb=" O ARG B 452 " pdb=" NH2 ARG B 456 " model vdw 2.364 3.120 nonbonded pdb=" O ASP B 135 " pdb=" N GLN B 141 " model vdw 2.376 3.120 nonbonded pdb=" O ARG B 386 " pdb=" OG1 THR B 389 " model vdw 2.537 3.040 nonbonded pdb=" O ARG B 106 " pdb=" OH TYR B 292 " model vdw 2.541 3.040 ... (remaining 20343 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.010 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 : 0.003 0.021 2644 Z= 0.137 Angle : 0.531 8.001 3617 Z= 0.300 Chirality : 0.034 0.140 412 Planarity : 0.004 0.041 430 Dihedral : 13.584 82.449 837 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 8.70 % Allowed : 7.91 % Favored : 83.40 % 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: 1.83 (0.48), residues: 315 helix: 2.00 (0.31), residues: 267 sheet: None (None), residues: 0 loop : -3.57 (0.81), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 166 HIS 0.002 0.001 HIS B 329 PHE 0.010 0.001 PHE B 380 TYR 0.013 0.001 TYR B 297 ARG 0.001 0.000 ARG B 358 Details of bonding type rmsd hydrogen bonds : bond 0.08642 ( 218) hydrogen bonds : angle 4.43576 ( 648) covalent geometry : bond 0.00280 ( 2644) covalent geometry : angle 0.53078 ( 3617) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.260 Fit side-chains REVERT: B 361 ARG cc_start: 0.6125 (tpp80) cc_final: 0.3801 (ptm-80) REVERT: B 369 TYR cc_start: 0.7269 (m-80) cc_final: 0.6968 (m-80) REVERT: B 370 MET cc_start: 0.6007 (mtm) cc_final: 0.5716 (mmt) REVERT: B 457 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8159 (tp) REVERT: B 492 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7248 (mp) outliers start: 22 outliers final: 6 residues processed: 92 average time/residue: 0.1703 time to fit residues: 18.1589 Evaluate side-chains 58 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 0.0970 chunk 29 optimal weight: 0.0570 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 GLN B 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.163941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.148914 restraints weight = 3506.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.152347 restraints weight = 1881.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.154373 restraints weight = 1237.542| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2644 Z= 0.144 Angle : 0.568 7.198 3617 Z= 0.291 Chirality : 0.037 0.153 412 Planarity : 0.003 0.030 430 Dihedral : 7.347 45.949 358 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 7.51 % Allowed : 12.65 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.48), residues: 315 helix: 1.97 (0.31), residues: 269 sheet: None (None), residues: 0 loop : -3.44 (0.77), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 378 HIS 0.002 0.001 HIS B 329 PHE 0.016 0.001 PHE B 462 TYR 0.013 0.001 TYR B 297 ARG 0.003 0.000 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 218) hydrogen bonds : angle 4.10120 ( 648) covalent geometry : bond 0.00323 ( 2644) covalent geometry : angle 0.56756 ( 3617) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.291 Fit side-chains REVERT: B 115 ILE cc_start: 0.5816 (mp) cc_final: 0.5542 (mt) REVERT: B 129 ASP cc_start: 0.7954 (m-30) cc_final: 0.7704 (m-30) REVERT: B 295 MET cc_start: 0.6718 (tmm) cc_final: 0.6400 (tmm) REVERT: B 361 ARG cc_start: 0.5576 (tpp80) cc_final: 0.3631 (ptm-80) REVERT: B 369 TYR cc_start: 0.7311 (m-80) cc_final: 0.6990 (m-80) REVERT: B 454 ARG cc_start: 0.7557 (ttm110) cc_final: 0.6126 (mmt180) outliers start: 19 outliers final: 9 residues processed: 69 average time/residue: 0.1433 time to fit residues: 11.8686 Evaluate side-chains 56 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 329 HIS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 479 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 24 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN 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 = 0.161894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.146654 restraints weight = 3739.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.149828 restraints weight = 2085.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.151714 restraints weight = 1408.559| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2644 Z= 0.139 Angle : 0.544 7.834 3617 Z= 0.281 Chirality : 0.038 0.270 412 Planarity : 0.003 0.029 430 Dihedral : 6.407 47.382 351 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 5.53 % Allowed : 17.00 % Favored : 77.47 % 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: 1.69 (0.48), residues: 315 helix: 1.86 (0.31), residues: 270 sheet: None (None), residues: 0 loop : -3.68 (0.72), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 378 HIS 0.002 0.001 HIS B 418 PHE 0.027 0.001 PHE B 393 TYR 0.014 0.001 TYR B 297 ARG 0.002 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 218) hydrogen bonds : angle 4.02071 ( 648) covalent geometry : bond 0.00305 ( 2644) covalent geometry : angle 0.54353 ( 3617) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.258 Fit side-chains REVERT: B 129 ASP cc_start: 0.7986 (m-30) cc_final: 0.7721 (m-30) REVERT: B 281 ARG cc_start: 0.7595 (ttm170) cc_final: 0.7244 (ptm160) REVERT: B 295 MET cc_start: 0.6839 (tmm) cc_final: 0.6563 (tmm) REVERT: B 361 ARG cc_start: 0.5514 (tpp80) cc_final: 0.3573 (ptm-80) REVERT: B 369 TYR cc_start: 0.7239 (m-80) cc_final: 0.7001 (m-80) REVERT: B 454 ARG cc_start: 0.7493 (ttm110) cc_final: 0.6084 (mmt180) REVERT: B 492 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6724 (mp) outliers start: 14 outliers final: 9 residues processed: 62 average time/residue: 0.1536 time to fit residues: 11.1999 Evaluate side-chains 56 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.0060 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.162374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.147371 restraints weight = 3712.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.150311 restraints weight = 2057.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.152609 restraints weight = 1404.993| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2644 Z= 0.127 Angle : 0.538 7.292 3617 Z= 0.279 Chirality : 0.038 0.269 412 Planarity : 0.003 0.028 430 Dihedral : 5.964 47.799 349 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 5.14 % Allowed : 16.60 % 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: 1.92 (0.48), residues: 315 helix: 1.97 (0.31), residues: 267 sheet: None (None), residues: 0 loop : -2.91 (0.83), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 378 HIS 0.002 0.001 HIS B 418 PHE 0.008 0.001 PHE B 380 TYR 0.012 0.001 TYR B 297 ARG 0.002 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 218) hydrogen bonds : angle 3.96906 ( 648) covalent geometry : bond 0.00271 ( 2644) covalent geometry : angle 0.53791 ( 3617) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.265 Fit side-chains REVERT: B 129 ASP cc_start: 0.7931 (m-30) cc_final: 0.7664 (m-30) REVERT: B 295 MET cc_start: 0.6805 (tmm) cc_final: 0.6500 (tmm) REVERT: B 361 ARG cc_start: 0.5389 (tpp80) cc_final: 0.3500 (ptm-80) REVERT: B 369 TYR cc_start: 0.7228 (m-80) cc_final: 0.6841 (m-80) REVERT: B 454 ARG cc_start: 0.7381 (ttm110) cc_final: 0.6060 (mmt180) REVERT: B 492 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6763 (mp) outliers start: 13 outliers final: 10 residues processed: 58 average time/residue: 0.1387 time to fit residues: 9.7570 Evaluate side-chains 59 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 4 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.163238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.147903 restraints weight = 3675.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.151084 restraints weight = 2060.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.153214 restraints weight = 1393.985| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2644 Z= 0.127 Angle : 0.542 7.516 3617 Z= 0.279 Chirality : 0.037 0.248 412 Planarity : 0.003 0.027 430 Dihedral : 5.927 49.198 349 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.35 % Allowed : 18.58 % Favored : 77.08 % 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: 1.97 (0.48), residues: 315 helix: 2.00 (0.31), residues: 267 sheet: None (None), residues: 0 loop : -2.87 (0.86), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 378 HIS 0.002 0.001 HIS B 418 PHE 0.022 0.001 PHE B 150 TYR 0.013 0.001 TYR B 297 ARG 0.002 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 218) hydrogen bonds : angle 3.93907 ( 648) covalent geometry : bond 0.00270 ( 2644) covalent geometry : angle 0.54228 ( 3617) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.260 Fit side-chains REVERT: B 115 ILE cc_start: 0.5970 (mp) cc_final: 0.5676 (mt) REVERT: B 129 ASP cc_start: 0.7890 (m-30) cc_final: 0.7613 (m-30) REVERT: B 295 MET cc_start: 0.6809 (tmm) cc_final: 0.6534 (tmm) REVERT: B 361 ARG cc_start: 0.5376 (tpp80) cc_final: 0.3493 (ptm-80) REVERT: B 369 TYR cc_start: 0.7065 (m-80) cc_final: 0.6828 (m-80) REVERT: B 448 VAL cc_start: 0.5624 (m) cc_final: 0.5364 (t) REVERT: B 454 ARG cc_start: 0.7367 (ttm110) cc_final: 0.6103 (mmt180) REVERT: B 492 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6801 (mp) REVERT: B 512 PHE cc_start: 0.4589 (t80) cc_final: 0.4369 (t80) outliers start: 11 outliers final: 9 residues processed: 57 average time/residue: 0.1525 time to fit residues: 10.3597 Evaluate side-chains 60 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.160621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145525 restraints weight = 3769.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.148351 restraints weight = 2235.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.149915 restraints weight = 1573.805| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2644 Z= 0.135 Angle : 0.560 7.531 3617 Z= 0.286 Chirality : 0.037 0.190 412 Planarity : 0.003 0.027 430 Dihedral : 5.964 51.099 349 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.35 % Allowed : 18.18 % Favored : 77.47 % 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: 1.85 (0.48), residues: 315 helix: 1.92 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -3.07 (0.86), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 378 HIS 0.002 0.001 HIS B 418 PHE 0.008 0.001 PHE B 380 TYR 0.015 0.001 TYR B 297 ARG 0.003 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 218) hydrogen bonds : angle 3.98373 ( 648) covalent geometry : bond 0.00294 ( 2644) covalent geometry : angle 0.55985 ( 3617) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.286 Fit side-chains REVERT: B 115 ILE cc_start: 0.5958 (mp) cc_final: 0.5732 (mt) REVERT: B 129 ASP cc_start: 0.7786 (m-30) cc_final: 0.7543 (m-30) REVERT: B 295 MET cc_start: 0.6792 (tmm) cc_final: 0.6510 (tmm) REVERT: B 361 ARG cc_start: 0.5441 (tpp80) cc_final: 0.3592 (ptm-80) REVERT: B 369 TYR cc_start: 0.7137 (m-80) cc_final: 0.6896 (m-80) REVERT: B 454 ARG cc_start: 0.7313 (ttm110) cc_final: 0.6112 (mmt180) REVERT: B 492 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6859 (mp) REVERT: B 512 PHE cc_start: 0.4486 (t80) cc_final: 0.4241 (t80) outliers start: 11 outliers final: 8 residues processed: 57 average time/residue: 0.1539 time to fit residues: 10.4125 Evaluate side-chains 56 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.160781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.145581 restraints weight = 3826.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.148117 restraints weight = 2264.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.150329 restraints weight = 1619.773| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2644 Z= 0.126 Angle : 0.549 7.438 3617 Z= 0.283 Chirality : 0.035 0.138 412 Planarity : 0.003 0.027 430 Dihedral : 5.491 51.850 347 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.95 % Allowed : 18.97 % Favored : 77.08 % 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: 1.80 (0.48), residues: 315 helix: 1.89 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -3.05 (0.86), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 378 HIS 0.002 0.001 HIS B 418 PHE 0.025 0.001 PHE B 150 TYR 0.013 0.001 TYR B 297 ARG 0.002 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 218) hydrogen bonds : angle 3.97915 ( 648) covalent geometry : bond 0.00269 ( 2644) covalent geometry : angle 0.54920 ( 3617) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.294 Fit side-chains REVERT: B 115 ILE cc_start: 0.5891 (mp) cc_final: 0.5675 (mt) REVERT: B 129 ASP cc_start: 0.7772 (m-30) cc_final: 0.7549 (m-30) REVERT: B 144 TRP cc_start: 0.7563 (m-10) cc_final: 0.7273 (m-10) REVERT: B 295 MET cc_start: 0.6771 (tmm) cc_final: 0.6491 (tmm) REVERT: B 361 ARG cc_start: 0.5394 (tpp80) cc_final: 0.3570 (ptm-80) REVERT: B 369 TYR cc_start: 0.7141 (m-80) cc_final: 0.6469 (m-80) REVERT: B 448 VAL cc_start: 0.5427 (m) cc_final: 0.5151 (t) REVERT: B 454 ARG cc_start: 0.7291 (ttm110) cc_final: 0.6107 (mmt180) REVERT: B 512 PHE cc_start: 0.4530 (t80) cc_final: 0.4216 (t80) outliers start: 10 outliers final: 10 residues processed: 61 average time/residue: 0.1622 time to fit residues: 11.8604 Evaluate side-chains 61 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 479 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.159588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144876 restraints weight = 3719.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.147364 restraints weight = 2196.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.149347 restraints weight = 1570.442| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2644 Z= 0.140 Angle : 0.587 8.077 3617 Z= 0.300 Chirality : 0.036 0.128 412 Planarity : 0.003 0.027 430 Dihedral : 5.573 52.908 347 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.74 % Allowed : 18.18 % Favored : 77.08 % 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: 1.70 (0.48), residues: 315 helix: 1.84 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -3.19 (0.83), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 378 HIS 0.002 0.001 HIS B 418 PHE 0.023 0.001 PHE B 150 TYR 0.015 0.001 TYR B 297 ARG 0.002 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 218) hydrogen bonds : angle 4.01115 ( 648) covalent geometry : bond 0.00310 ( 2644) covalent geometry : angle 0.58702 ( 3617) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.272 Fit side-chains REVERT: B 115 ILE cc_start: 0.5910 (mp) cc_final: 0.5676 (mt) REVERT: B 129 ASP cc_start: 0.7762 (m-30) cc_final: 0.7504 (m-30) REVERT: B 144 TRP cc_start: 0.7566 (m-10) cc_final: 0.7281 (m-10) REVERT: B 361 ARG cc_start: 0.5484 (OUTLIER) cc_final: 0.3623 (ptm-80) REVERT: B 369 TYR cc_start: 0.7041 (m-80) cc_final: 0.6487 (m-80) REVERT: B 398 GLN cc_start: 0.6720 (pm20) cc_final: 0.6513 (pm20) REVERT: B 448 VAL cc_start: 0.5431 (m) cc_final: 0.5148 (t) REVERT: B 454 ARG cc_start: 0.7307 (ttm110) cc_final: 0.6083 (mmt180) REVERT: B 461 TYR cc_start: 0.7178 (m-10) cc_final: 0.6806 (m-10) REVERT: B 492 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6797 (mp) REVERT: B 512 PHE cc_start: 0.4491 (t80) cc_final: 0.4158 (t80) outliers start: 12 outliers final: 9 residues processed: 60 average time/residue: 0.1592 time to fit residues: 11.3849 Evaluate side-chains 59 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.159920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145345 restraints weight = 3711.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147857 restraints weight = 2179.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.149984 restraints weight = 1545.493| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2644 Z= 0.132 Angle : 0.563 6.872 3617 Z= 0.293 Chirality : 0.037 0.190 412 Planarity : 0.003 0.027 430 Dihedral : 5.519 53.056 347 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 5.14 % Allowed : 18.18 % Favored : 76.68 % 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: 1.84 (0.48), residues: 315 helix: 1.95 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -3.24 (0.82), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 378 HIS 0.002 0.000 HIS B 418 PHE 0.024 0.001 PHE B 150 TYR 0.021 0.001 TYR B 461 ARG 0.002 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 218) hydrogen bonds : angle 3.99132 ( 648) covalent geometry : bond 0.00287 ( 2644) covalent geometry : angle 0.56323 ( 3617) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.253 Fit side-chains REVERT: B 115 ILE cc_start: 0.5901 (mp) cc_final: 0.5659 (mt) REVERT: B 129 ASP cc_start: 0.7778 (m-30) cc_final: 0.7536 (m-30) REVERT: B 144 TRP cc_start: 0.7592 (m-10) cc_final: 0.7304 (m-10) REVERT: B 166 TRP cc_start: 0.6970 (p90) cc_final: 0.5602 (t-100) REVERT: B 361 ARG cc_start: 0.5472 (OUTLIER) cc_final: 0.3598 (ptm-80) REVERT: B 369 TYR cc_start: 0.7051 (m-80) cc_final: 0.6490 (m-80) REVERT: B 448 VAL cc_start: 0.5444 (m) cc_final: 0.5128 (t) REVERT: B 454 ARG cc_start: 0.7303 (ttm110) cc_final: 0.6096 (mmt180) REVERT: B 466 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.6978 (tp) REVERT: B 492 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6753 (mp) REVERT: B 512 PHE cc_start: 0.4504 (t80) cc_final: 0.4254 (t80) outliers start: 13 outliers final: 9 residues processed: 62 average time/residue: 0.1424 time to fit residues: 10.5665 Evaluate side-chains 63 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.0070 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.159156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.144635 restraints weight = 3695.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.147331 restraints weight = 2177.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.149231 restraints weight = 1529.455| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2644 Z= 0.142 Angle : 0.584 7.260 3617 Z= 0.304 Chirality : 0.038 0.225 412 Planarity : 0.003 0.027 430 Dihedral : 5.564 53.690 347 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.74 % Allowed : 18.18 % Favored : 77.08 % 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: 1.77 (0.48), residues: 315 helix: 1.91 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -3.37 (0.80), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 378 HIS 0.002 0.001 HIS B 418 PHE 0.023 0.001 PHE B 150 TYR 0.015 0.001 TYR B 297 ARG 0.002 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 218) hydrogen bonds : angle 4.04391 ( 648) covalent geometry : bond 0.00312 ( 2644) covalent geometry : angle 0.58412 ( 3617) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.314 Fit side-chains REVERT: B 115 ILE cc_start: 0.5917 (mp) cc_final: 0.5694 (mt) REVERT: B 129 ASP cc_start: 0.7780 (m-30) cc_final: 0.7531 (m-30) REVERT: B 144 TRP cc_start: 0.7606 (m-10) cc_final: 0.7312 (m-10) REVERT: B 166 TRP cc_start: 0.6976 (p90) cc_final: 0.5645 (t-100) REVERT: B 361 ARG cc_start: 0.5500 (OUTLIER) cc_final: 0.3638 (ptm-80) REVERT: B 369 TYR cc_start: 0.7038 (m-80) cc_final: 0.6465 (m-80) REVERT: B 398 GLN cc_start: 0.6744 (pm20) cc_final: 0.6358 (pm20) REVERT: B 448 VAL cc_start: 0.5467 (m) cc_final: 0.5149 (t) REVERT: B 454 ARG cc_start: 0.7342 (ttm110) cc_final: 0.6132 (mmt180) REVERT: B 466 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7022 (tp) REVERT: B 492 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6804 (mp) REVERT: B 512 PHE cc_start: 0.4442 (t80) cc_final: 0.4206 (t80) outliers start: 12 outliers final: 9 residues processed: 60 average time/residue: 0.1513 time to fit residues: 10.8498 Evaluate side-chains 61 residues out of total 280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 PHE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 378 TRP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 479 LYS Chi-restraints excluded: chain B residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.159198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.144447 restraints weight = 3767.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.147020 restraints weight = 2200.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.149126 restraints weight = 1553.643| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2644 Z= 0.139 Angle : 0.588 7.181 3617 Z= 0.309 Chirality : 0.037 0.210 412 Planarity : 0.003 0.027 430 Dihedral : 5.538 53.548 347 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 5.14 % Allowed : 18.58 % Favored : 76.28 % 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: 1.75 (0.48), residues: 315 helix: 1.91 (0.31), residues: 268 sheet: None (None), residues: 0 loop : -3.46 (0.79), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 378 HIS 0.002 0.001 HIS B 418 PHE 0.023 0.001 PHE B 150 TYR 0.013 0.001 TYR B 297 ARG 0.002 0.000 ARG B 456 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 218) hydrogen bonds : angle 4.01052 ( 648) covalent geometry : bond 0.00302 ( 2644) covalent geometry : angle 0.58800 ( 3617) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1304.99 seconds wall clock time: 23 minutes 11.81 seconds (1391.81 seconds total)