Starting phenix.real_space_refine on Mon Feb 10 22:32:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7s_39826/02_2025/8z7s_39826.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7s_39826/02_2025/8z7s_39826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7s_39826/02_2025/8z7s_39826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7s_39826/02_2025/8z7s_39826.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7s_39826/02_2025/8z7s_39826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7s_39826/02_2025/8z7s_39826.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.116 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 16 5.16 5 C 2103 2.51 5 N 467 2.21 5 O 530 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-5592/modules/chem_data/mon_lib" Total number of atoms: 3116 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3098 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'VIB': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.64, per 1000 atoms: 0.85 Number of scatterers: 3116 At special positions: 0 Unit cell: (62, 67, 68, 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 16 16.00 O 530 8.00 N 467 7.00 C 2103 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: 0.93 Conformation dependent library (CDL) restraints added in 466.8 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 86.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 34 through 40 Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.507A pdb=" N ILE A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.760A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 79 through 99 removed outlier: 3.571A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 129 removed outlier: 3.947A pdb=" N THR A 105 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 165 removed outlier: 3.656A pdb=" N ARG A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.513A pdb=" N PHE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 277 through 307 removed outlier: 4.222A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 337 removed outlier: 3.903A pdb=" N GLY A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 366 removed outlier: 3.502A pdb=" N THR A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 398 Processing helix chain 'A' and resid 402 through 426 removed outlier: 3.665A pdb=" N VAL A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 461 removed outlier: 3.737A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 741 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: 0.88 Time building geometry restraints manager: 1.02 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: 892 1.34 - 1.46: 733 1.46 - 1.57: 1557 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 3210 Sorted by residual: bond pdb=" N TYR A 445 " pdb=" CA TYR A 445 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.17e+00 bond pdb=" C2 VIB A 501 " pdb=" S1 VIB A 501 " ideal model delta sigma weight residual 1.670 1.715 -0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" N SER A 382 " pdb=" CA SER A 382 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.02e+00 bond pdb=" CA SER A 382 " pdb=" CB SER A 382 " ideal model delta sigma weight residual 1.529 1.506 0.023 1.55e-02 4.16e+03 2.15e+00 bond pdb=" CA LEU A 68 " pdb=" C LEU A 68 " ideal model delta sigma weight residual 1.520 1.536 -0.016 1.23e-02 6.61e+03 1.60e+00 ... (remaining 3205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 4254 1.28 - 2.55: 102 2.55 - 3.83: 19 3.83 - 5.10: 8 5.10 - 6.38: 5 Bond angle restraints: 4388 Sorted by residual: angle pdb=" N TYR A 445 " pdb=" CA TYR A 445 " pdb=" C TYR A 445 " ideal model delta sigma weight residual 111.07 108.25 2.82 1.07e+00 8.73e-01 6.97e+00 angle pdb=" CA SER A 382 " pdb=" C SER A 382 " pdb=" O SER A 382 " ideal model delta sigma weight residual 120.82 118.16 2.66 1.05e+00 9.07e-01 6.42e+00 angle pdb=" CA ASN A 399 " pdb=" CB ASN A 399 " pdb=" CG ASN A 399 " ideal model delta sigma weight residual 112.60 115.07 -2.47 1.00e+00 1.00e+00 6.08e+00 angle pdb=" CA TYR A 280 " pdb=" CB TYR A 280 " pdb=" CG TYR A 280 " ideal model delta sigma weight residual 113.90 118.11 -4.21 1.80e+00 3.09e-01 5.48e+00 angle pdb=" O SER A 382 " pdb=" C SER A 382 " pdb=" N TYR A 383 " ideal model delta sigma weight residual 122.07 124.46 -2.39 1.03e+00 9.43e-01 5.40e+00 ... (remaining 4383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 1533 16.59 - 33.19: 210 33.19 - 49.78: 50 49.78 - 66.37: 13 66.37 - 82.97: 6 Dihedral angle restraints: 1812 sinusoidal: 663 harmonic: 1149 Sorted by residual: dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ILE A 424 " pdb=" C ILE A 424 " pdb=" N VAL A 425 " pdb=" CA VAL A 425 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASP A 75 " pdb=" CB ASP A 75 " pdb=" CG ASP A 75 " pdb=" OD1 ASP A 75 " ideal model delta sinusoidal sigma weight residual -30.00 -85.07 55.07 1 2.00e+01 2.50e-03 1.03e+01 ... (remaining 1809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 330 0.034 - 0.067: 127 0.067 - 0.101: 31 0.101 - 0.134: 13 0.134 - 0.168: 4 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA ASN A 399 " pdb=" N ASN A 399 " pdb=" C ASN A 399 " pdb=" CB ASN A 399 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CB ILE A 127 " pdb=" CA ILE A 127 " pdb=" CG1 ILE A 127 " pdb=" CG2 ILE A 127 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA VAL A 261 " pdb=" N VAL A 261 " pdb=" C VAL A 261 " pdb=" CB VAL A 261 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 502 not shown) Planarity restraints: 525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 VIB A 501 " -0.148 2.00e-02 2.50e+03 2.61e-01 1.36e+03 pdb=" C4 VIB A 501 " -0.112 2.00e-02 2.50e+03 pdb=" C5 VIB A 501 " 0.039 2.00e-02 2.50e+03 pdb=" C6 VIB A 501 " 0.392 2.00e-02 2.50e+03 pdb=" C7A VIB A 501 " 0.393 2.00e-02 2.50e+03 pdb=" CM4 VIB A 501 " -0.384 2.00e-02 2.50e+03 pdb=" N3 VIB A 501 " 0.043 2.00e-02 2.50e+03 pdb=" S1 VIB A 501 " -0.222 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 150 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C ALA A 150 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA A 150 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR A 151 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 146 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.61e+00 pdb=" C VAL A 146 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 146 " -0.010 2.00e-02 2.50e+03 pdb=" N THR A 147 " -0.009 2.00e-02 2.50e+03 ... (remaining 522 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 667 2.77 - 3.30: 3261 3.30 - 3.83: 5719 3.83 - 4.37: 6630 4.37 - 4.90: 11294 Nonbonded interactions: 27571 Sorted by model distance: nonbonded pdb=" OH TYR A 128 " pdb=" OG SER A 140 " model vdw 2.234 3.040 nonbonded pdb=" O VAL A 70 " pdb=" OG1 THR A 74 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR A 126 " pdb=" O PRO A 191 " model vdw 2.265 3.040 nonbonded pdb=" O GLN A 393 " pdb=" ND2 ASN A 397 " model vdw 2.319 3.120 nonbonded pdb=" NE2 GLN A 300 " pdb=" OE1 GLU A 320 " model vdw 2.320 3.120 ... (remaining 27566 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.330 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 0.045 3210 Z= 0.267 Angle : 0.555 6.378 4388 Z= 0.308 Chirality : 0.041 0.168 505 Planarity : 0.012 0.261 525 Dihedral : 16.814 82.968 1078 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.30 % Allowed : 23.12 % Favored : 76.58 % 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: 0.35 (0.41), residues: 383 helix: 0.35 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.36 (0.94), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.021 0.001 PHE A 71 TYR 0.018 0.001 TYR A 280 ARG 0.001 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.327 Fit side-chains REVERT: A 384 MET cc_start: 0.8982 (mmt) cc_final: 0.8611 (mmt) outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.1342 time to fit residues: 7.6252 Evaluate side-chains 39 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 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 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.139024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.114345 restraints weight = 3420.317| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.59 r_work: 0.3219 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3210 Z= 0.271 Angle : 0.615 9.452 4388 Z= 0.325 Chirality : 0.043 0.171 505 Planarity : 0.004 0.033 525 Dihedral : 5.980 85.853 428 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.60 % Allowed : 19.82 % Favored : 76.58 % 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: 2.03 (0.43), residues: 383 helix: 1.47 (0.28), residues: 325 sheet: None (None), residues: 0 loop : 1.04 (0.95), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 94 HIS 0.004 0.001 HIS A 364 PHE 0.021 0.002 PHE A 71 TYR 0.018 0.002 TYR A 280 ARG 0.002 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.326 Fit side-chains REVERT: A 266 PHE cc_start: 0.7095 (m-80) cc_final: 0.5928 (t80) REVERT: A 271 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7383 (tt0) REVERT: A 437 ILE cc_start: 0.8474 (tp) cc_final: 0.8128 (tp) REVERT: A 458 MET cc_start: 0.7612 (mmp) cc_final: 0.7396 (mmm) outliers start: 12 outliers final: 6 residues processed: 55 average time/residue: 0.1124 time to fit residues: 8.0894 Evaluate side-chains 44 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 460 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.141932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117547 restraints weight = 3385.519| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.57 r_work: 0.3216 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3210 Z= 0.237 Angle : 0.562 5.231 4388 Z= 0.301 Chirality : 0.042 0.174 505 Planarity : 0.004 0.034 525 Dihedral : 5.910 85.995 427 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.00 % Allowed : 21.32 % Favored : 75.68 % 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: 2.16 (0.43), residues: 383 helix: 1.56 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 1.13 (0.95), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.021 0.001 PHE A 71 TYR 0.017 0.002 TYR A 280 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.305 Fit side-chains REVERT: A 384 MET cc_start: 0.8912 (mmt) cc_final: 0.8448 (mmt) REVERT: A 458 MET cc_start: 0.7596 (mmp) cc_final: 0.7366 (mmm) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 0.1255 time to fit residues: 7.7247 Evaluate side-chains 44 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 460 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 11 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.143887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119571 restraints weight = 3423.532| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.59 r_work: 0.3246 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3210 Z= 0.188 Angle : 0.523 5.123 4388 Z= 0.284 Chirality : 0.041 0.165 505 Planarity : 0.004 0.031 525 Dihedral : 5.820 84.371 427 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.30 % Allowed : 21.92 % Favored : 74.77 % 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: 2.38 (0.43), residues: 383 helix: 1.70 (0.28), residues: 324 sheet: None (None), residues: 0 loop : 1.24 (0.96), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.019 0.001 PHE A 71 TYR 0.018 0.001 TYR A 280 ARG 0.001 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.316 Fit side-chains REVERT: A 384 MET cc_start: 0.8906 (mmt) cc_final: 0.8579 (mmt) REVERT: A 458 MET cc_start: 0.7545 (mmp) cc_final: 0.7327 (mmm) outliers start: 11 outliers final: 7 residues processed: 55 average time/residue: 0.1132 time to fit residues: 8.2936 Evaluate side-chains 47 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 460 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112464 restraints weight = 3381.626| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.57 r_work: 0.3201 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3210 Z= 0.266 Angle : 0.568 7.284 4388 Z= 0.302 Chirality : 0.042 0.178 505 Planarity : 0.004 0.034 525 Dihedral : 5.834 83.813 427 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.60 % Allowed : 21.32 % Favored : 75.08 % 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: 2.24 (0.43), residues: 383 helix: 1.56 (0.28), residues: 325 sheet: None (None), residues: 0 loop : 1.49 (0.98), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.021 0.002 PHE A 71 TYR 0.018 0.002 TYR A 280 ARG 0.001 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.332 Fit side-chains REVERT: A 458 MET cc_start: 0.7546 (mmp) cc_final: 0.7321 (mmm) outliers start: 12 outliers final: 8 residues processed: 50 average time/residue: 0.1141 time to fit residues: 7.5537 Evaluate side-chains 49 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 457 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.141662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117095 restraints weight = 3475.275| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.60 r_work: 0.3208 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3210 Z= 0.235 Angle : 0.554 7.608 4388 Z= 0.294 Chirality : 0.042 0.177 505 Planarity : 0.004 0.034 525 Dihedral : 5.795 83.051 427 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.30 % Allowed : 22.52 % Favored : 74.17 % 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: 2.37 (0.43), residues: 383 helix: 1.65 (0.28), residues: 325 sheet: None (None), residues: 0 loop : 1.55 (0.98), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.021 0.001 PHE A 71 TYR 0.017 0.001 TYR A 280 ARG 0.001 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.254 Fit side-chains REVERT: A 296 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8527 (mp) REVERT: A 384 MET cc_start: 0.8967 (mmt) cc_final: 0.8486 (mmt) outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 0.1191 time to fit residues: 7.8098 Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 457 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 9 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.141154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116694 restraints weight = 3353.983| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.61 r_work: 0.3205 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3210 Z= 0.204 Angle : 0.545 7.132 4388 Z= 0.288 Chirality : 0.041 0.166 505 Planarity : 0.004 0.032 525 Dihedral : 5.746 82.684 427 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.60 % Allowed : 21.92 % Favored : 74.47 % 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: 2.52 (0.43), residues: 383 helix: 1.74 (0.28), residues: 325 sheet: None (None), residues: 0 loop : 1.64 (0.98), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.019 0.001 PHE A 71 TYR 0.017 0.001 TYR A 280 ARG 0.000 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.370 Fit side-chains REVERT: A 383 TYR cc_start: 0.8823 (t80) cc_final: 0.8567 (t80) REVERT: A 384 MET cc_start: 0.8946 (mmt) cc_final: 0.8652 (mmt) outliers start: 12 outliers final: 10 residues processed: 52 average time/residue: 0.1148 time to fit residues: 7.8913 Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 457 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 7 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.142545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117933 restraints weight = 3380.294| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.60 r_work: 0.3230 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3210 Z= 0.221 Angle : 0.553 6.806 4388 Z= 0.292 Chirality : 0.041 0.170 505 Planarity : 0.004 0.032 525 Dihedral : 5.745 82.587 427 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.90 % Allowed : 21.92 % Favored : 74.17 % 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 (0.43), residues: 383 helix: 1.69 (0.28), residues: 326 sheet: None (None), residues: 0 loop : 1.72 (0.99), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.020 0.001 PHE A 71 TYR 0.017 0.001 TYR A 280 ARG 0.000 0.000 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.318 Fit side-chains REVERT: A 296 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8443 (mp) REVERT: A 383 TYR cc_start: 0.8887 (t80) cc_final: 0.8656 (t80) REVERT: A 384 MET cc_start: 0.8970 (mmt) cc_final: 0.8666 (mmt) outliers start: 13 outliers final: 10 residues processed: 53 average time/residue: 0.1162 time to fit residues: 8.0950 Evaluate side-chains 51 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 457 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 3 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.0060 chunk 29 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.142981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118563 restraints weight = 3333.389| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.61 r_work: 0.3211 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3210 Z= 0.188 Angle : 0.560 8.910 4388 Z= 0.288 Chirality : 0.040 0.164 505 Planarity : 0.004 0.031 525 Dihedral : 5.711 82.764 427 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.60 % Allowed : 22.52 % Favored : 73.87 % 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: 2.66 (0.43), residues: 383 helix: 1.83 (0.28), residues: 326 sheet: None (None), residues: 0 loop : 1.73 (0.99), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.018 0.001 PHE A 71 TYR 0.016 0.001 TYR A 280 ARG 0.001 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.317 Fit side-chains REVERT: A 296 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8361 (mp) REVERT: A 383 TYR cc_start: 0.8750 (t80) cc_final: 0.8516 (t80) REVERT: A 384 MET cc_start: 0.8915 (mmt) cc_final: 0.8628 (mmt) REVERT: A 458 MET cc_start: 0.7489 (mmp) cc_final: 0.7276 (mmt) outliers start: 12 outliers final: 10 residues processed: 49 average time/residue: 0.1190 time to fit residues: 7.6528 Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 457 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.0030 chunk 17 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.119937 restraints weight = 3340.902| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.54 r_work: 0.3204 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3210 Z= 0.209 Angle : 0.568 9.015 4388 Z= 0.293 Chirality : 0.041 0.164 505 Planarity : 0.004 0.032 525 Dihedral : 5.729 83.078 427 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.30 % Allowed : 23.12 % Favored : 73.57 % 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: 2.64 (0.43), residues: 383 helix: 1.81 (0.28), residues: 326 sheet: None (None), residues: 0 loop : 1.77 (0.99), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.018 0.001 PHE A 71 TYR 0.016 0.001 TYR A 280 ARG 0.000 0.000 ARG A 402 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.320 Fit side-chains REVERT: A 296 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8374 (mp) REVERT: A 383 TYR cc_start: 0.8843 (t80) cc_final: 0.8641 (t80) REVERT: A 384 MET cc_start: 0.8932 (mmt) cc_final: 0.8622 (mmt) outliers start: 11 outliers final: 10 residues processed: 49 average time/residue: 0.1181 time to fit residues: 7.7009 Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 444 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 0.4980 chunk 13 optimal weight: 0.0670 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120388 restraints weight = 3363.508| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.60 r_work: 0.3250 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3210 Z= 0.195 Angle : 0.565 9.331 4388 Z= 0.290 Chirality : 0.040 0.163 505 Planarity : 0.004 0.031 525 Dihedral : 5.734 83.590 427 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.30 % Allowed : 22.82 % Favored : 73.87 % 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: 2.74 (0.43), residues: 383 helix: 1.89 (0.28), residues: 326 sheet: None (None), residues: 0 loop : 1.77 (0.99), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 94 HIS 0.002 0.001 HIS A 364 PHE 0.017 0.001 PHE A 71 TYR 0.016 0.001 TYR A 280 ARG 0.000 0.000 ARG A 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.07 seconds wall clock time: 32 minutes 1.63 seconds (1921.63 seconds total)