Starting phenix.real_space_refine on Sun Apr 27 01:29:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ya3_39090/04_2025/8ya3_39090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ya3_39090/04_2025/8ya3_39090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ya3_39090/04_2025/8ya3_39090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ya3_39090/04_2025/8ya3_39090.map" model { file = "/net/cci-nas-00/data/ceres_data/8ya3_39090/04_2025/8ya3_39090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ya3_39090/04_2025/8ya3_39090.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 15 5.16 5 C 2700 2.51 5 N 668 2.21 5 O 677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 4060 Number of models: 1 Model: "" Number of chains: 3 Chain: "Y" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3165 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 20, 'TRANS': 385} Chain breaks: 2 Chain: "E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 480 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "B" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain breaks: 2 Time building chain proxies: 3.09, per 1000 atoms: 0.76 Number of scatterers: 4060 At special positions: 0 Unit cell: (91.524, 69.432, 88.368, 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 15 16.00 O 677 8.00 N 668 7.00 C 2700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 500.5 milliseconds 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 954 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 1 sheets defined 71.9% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'Y' and resid 2 through 11 Processing helix chain 'Y' and resid 11 through 33 Processing helix chain 'Y' and resid 74 through 88 removed outlier: 3.568A pdb=" N GLN Y 88 " --> pdb=" O VAL Y 84 " (cutoff:3.500A) Processing helix chain 'Y' and resid 92 through 100 Processing helix chain 'Y' and resid 102 through 134 Processing helix chain 'Y' and resid 145 through 173 Processing helix chain 'Y' and resid 177 through 202 removed outlier: 3.647A pdb=" N ILE Y 181 " --> pdb=" O ASN Y 177 " (cutoff:3.500A) Proline residue: Y 192 - end of helix Processing helix chain 'Y' and resid 213 through 236 Processing helix chain 'Y' and resid 271 through 292 Proline residue: Y 284 - end of helix removed outlier: 3.519A pdb=" N GLY Y 292 " --> pdb=" O ALA Y 288 " (cutoff:3.500A) Processing helix chain 'Y' and resid 294 through 304 removed outlier: 3.579A pdb=" N LEU Y 298 " --> pdb=" O ASN Y 294 " (cutoff:3.500A) Processing helix chain 'Y' and resid 310 through 331 removed outlier: 3.651A pdb=" N ILE Y 314 " --> pdb=" O VAL Y 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 332 through 343 removed outlier: 3.553A pdb=" N GLN Y 343 " --> pdb=" O ASN Y 339 " (cutoff:3.500A) Processing helix chain 'Y' and resid 353 through 390 removed outlier: 4.028A pdb=" N GLN Y 357 " --> pdb=" O GLY Y 353 " (cutoff:3.500A) Proline residue: Y 382 - end of helix removed outlier: 3.883A pdb=" N PHE Y 388 " --> pdb=" O PHE Y 384 " (cutoff:3.500A) Processing helix chain 'Y' and resid 399 through 422 removed outlier: 3.907A pdb=" N LEU Y 403 " --> pdb=" O GLY Y 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 16 removed outlier: 3.562A pdb=" N LYS E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 59 Processing helix chain 'B' and resid 3 through 19 Processing helix chain 'B' and resid 36 through 41 Processing sheet with id=AA1, first strand: chain 'Y' and resid 261 through 265 removed outlier: 3.634A pdb=" N PHE Y 238 " --> pdb=" O SER E 19 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 861 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: 0.91 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1227 1.34 - 1.46: 811 1.46 - 1.57: 2084 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 4150 Sorted by residual: bond pdb=" CB THR Y 323 " pdb=" CG2 THR Y 323 " ideal model delta sigma weight residual 1.521 1.433 0.088 3.30e-02 9.18e+02 7.04e+00 bond pdb=" CG PRO Y 273 " pdb=" CD PRO Y 273 " ideal model delta sigma weight residual 1.503 1.431 0.072 3.40e-02 8.65e+02 4.43e+00 bond pdb=" CB PRO Y 76 " pdb=" CG PRO Y 76 " ideal model delta sigma weight residual 1.492 1.405 0.087 5.00e-02 4.00e+02 3.05e+00 bond pdb=" CA HIS Y 424 " pdb=" C HIS Y 424 " ideal model delta sigma weight residual 1.531 1.514 0.017 1.12e-02 7.97e+03 2.32e+00 bond pdb=" CB GLN Y 235 " pdb=" CG GLN Y 235 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.28e+00 ... (remaining 4145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 5299 1.74 - 3.47: 272 3.47 - 5.21: 52 5.21 - 6.95: 10 6.95 - 8.69: 5 Bond angle restraints: 5638 Sorted by residual: angle pdb=" N VAL Y 421 " pdb=" CA VAL Y 421 " pdb=" C VAL Y 421 " ideal model delta sigma weight residual 111.05 118.75 -7.70 1.25e+00 6.40e-01 3.79e+01 angle pdb=" C LEU Y 420 " pdb=" N VAL Y 421 " pdb=" CA VAL Y 421 " ideal model delta sigma weight residual 120.47 125.81 -5.34 1.58e+00 4.01e-01 1.14e+01 angle pdb=" CA PRO Y 284 " pdb=" C PRO Y 284 " pdb=" N PRO Y 285 " ideal model delta sigma weight residual 117.93 121.97 -4.04 1.20e+00 6.94e-01 1.13e+01 angle pdb=" C GLN Y 142 " pdb=" N ASN Y 143 " pdb=" CA ASN Y 143 " ideal model delta sigma weight residual 121.80 129.95 -8.15 2.44e+00 1.68e-01 1.12e+01 angle pdb=" C LYS Y 422 " pdb=" N ARG Y 423 " pdb=" CA ARG Y 423 " ideal model delta sigma weight residual 120.28 125.00 -4.72 1.44e+00 4.82e-01 1.07e+01 ... (remaining 5633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 2087 17.00 - 34.00: 257 34.00 - 51.00: 69 51.00 - 68.00: 6 68.00 - 84.99: 3 Dihedral angle restraints: 2422 sinusoidal: 939 harmonic: 1483 Sorted by residual: dihedral pdb=" CA GLY Y 344 " pdb=" C GLY Y 344 " pdb=" N GLY Y 345 " pdb=" CA GLY Y 345 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA PHE B 44 " pdb=" C PHE B 44 " pdb=" N GLU B 45 " pdb=" CA GLU B 45 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA GLN Y 65 " pdb=" C GLN Y 65 " pdb=" N ASN Y 66 " pdb=" CA ASN Y 66 " ideal model delta harmonic sigma weight residual 180.00 162.77 17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 2419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 386 0.039 - 0.079: 197 0.079 - 0.118: 64 0.118 - 0.157: 27 0.157 - 0.196: 8 Chirality restraints: 682 Sorted by residual: chirality pdb=" CB ILE Y 397 " pdb=" CA ILE Y 397 " pdb=" CG1 ILE Y 397 " pdb=" CG2 ILE Y 397 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.64e-01 chirality pdb=" CA VAL Y 36 " pdb=" N VAL Y 36 " pdb=" C VAL Y 36 " pdb=" CB VAL Y 36 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CA THR Y 323 " pdb=" N THR Y 323 " pdb=" C THR Y 323 " pdb=" CB THR Y 323 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 679 not shown) Planarity restraints: 689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO Y 284 " 0.049 5.00e-02 4.00e+02 7.22e-02 8.34e+00 pdb=" N PRO Y 285 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO Y 285 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO Y 285 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL Y 36 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO Y 37 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO Y 37 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO Y 37 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Y 391 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO Y 392 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO Y 392 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO Y 392 " -0.028 5.00e-02 4.00e+02 ... (remaining 686 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1102 2.79 - 3.32: 3770 3.32 - 3.85: 6689 3.85 - 4.37: 7019 4.37 - 4.90: 12452 Nonbonded interactions: 31032 Sorted by model distance: nonbonded pdb=" O LEU Y 364 " pdb=" OG1 THR Y 368 " model vdw 2.266 3.040 nonbonded pdb=" O TRP Y 299 " pdb=" OG1 THR Y 303 " model vdw 2.288 3.040 nonbonded pdb=" CZ PHE Y 280 " pdb=" CD1 LEU B 13 " model vdw 2.336 3.760 nonbonded pdb=" NE2 GLN Y 85 " pdb=" OH TYR Y 326 " model vdw 2.360 3.120 nonbonded pdb=" CE1 PHE Y 280 " pdb=" CD1 LEU B 13 " model vdw 2.385 3.760 ... (remaining 31027 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.060 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.009 0.088 4150 Z= 0.370 Angle : 0.933 8.687 5638 Z= 0.520 Chirality : 0.057 0.196 682 Planarity : 0.008 0.072 689 Dihedral : 15.754 84.995 1468 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.23 % Allowed : 21.77 % Favored : 78.00 % 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: -2.67 (0.31), residues: 505 helix: -1.30 (0.21), residues: 358 sheet: -0.13 (1.71), residues: 10 loop : -2.83 (0.50), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP Y 98 HIS 0.004 0.001 HIS B 67 PHE 0.019 0.002 PHE Y 328 TYR 0.013 0.002 TYR Y 326 ARG 0.002 0.000 ARG Y 366 Details of bonding type rmsd hydrogen bonds : bond 0.11954 ( 287) hydrogen bonds : angle 5.69910 ( 861) covalent geometry : bond 0.00898 ( 4150) covalent geometry : angle 0.93317 ( 5638) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 411 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7389 (tm-30) REVERT: E 54 LEU cc_start: 0.9074 (tp) cc_final: 0.8780 (tt) REVERT: B 49 LEU cc_start: 0.9302 (mt) cc_final: 0.8703 (mm) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 0.2235 time to fit residues: 16.0122 Evaluate side-chains 45 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 385 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 66 ASN Y 85 GLN Y 235 GLN Y 267 ASN Y 387 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.081778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.063608 restraints weight = 12013.754| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.73 r_work: 0.2989 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4150 Z= 0.135 Angle : 0.561 5.395 5638 Z= 0.301 Chirality : 0.041 0.151 682 Planarity : 0.005 0.048 689 Dihedral : 5.042 39.522 553 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.27 % Allowed : 22.22 % Favored : 75.51 % 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: 0.17 (0.36), residues: 505 helix: 0.99 (0.25), residues: 365 sheet: 0.32 (1.79), residues: 10 loop : -2.43 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 98 HIS 0.002 0.000 HIS Y 424 PHE 0.017 0.001 PHE Y 291 TYR 0.009 0.001 TYR Y 359 ARG 0.003 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.04830 ( 287) hydrogen bonds : angle 4.07953 ( 861) covalent geometry : bond 0.00287 ( 4150) covalent geometry : angle 0.56117 ( 5638) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: Y 250 GLU cc_start: 0.8041 (tt0) cc_final: 0.7766 (tm-30) REVERT: Y 326 TYR cc_start: 0.9078 (t80) cc_final: 0.8872 (t80) REVERT: E 54 LEU cc_start: 0.9014 (tp) cc_final: 0.8788 (tt) REVERT: B 43 MET cc_start: 0.7672 (ptp) cc_final: 0.7361 (ptp) outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 0.1701 time to fit residues: 13.5542 Evaluate side-chains 53 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.081946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.063957 restraints weight = 12019.572| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.66 r_work: 0.2996 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4150 Z= 0.136 Angle : 0.527 5.467 5638 Z= 0.280 Chirality : 0.041 0.145 682 Planarity : 0.004 0.044 689 Dihedral : 4.679 38.792 553 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.72 % Allowed : 22.90 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.38), residues: 505 helix: 1.85 (0.26), residues: 365 sheet: 0.56 (1.89), residues: 10 loop : -2.08 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 PHE 0.011 0.001 PHE Y 112 TYR 0.009 0.001 TYR Y 326 ARG 0.002 0.000 ARG Y 302 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 287) hydrogen bonds : angle 3.84411 ( 861) covalent geometry : bond 0.00304 ( 4150) covalent geometry : angle 0.52713 ( 5638) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.507 Fit side-chains REVERT: Y 72 MET cc_start: 0.9090 (mmm) cc_final: 0.8379 (tpt) REVERT: Y 90 ASP cc_start: 0.8197 (m-30) cc_final: 0.7832 (t0) REVERT: Y 130 TYR cc_start: 0.8313 (t80) cc_final: 0.8076 (t80) REVERT: E 10 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8728 (mm-30) REVERT: E 54 LEU cc_start: 0.9088 (tp) cc_final: 0.8850 (tt) REVERT: B 43 MET cc_start: 0.7704 (ptp) cc_final: 0.7440 (ptp) outliers start: 12 outliers final: 8 residues processed: 61 average time/residue: 0.1592 time to fit residues: 12.4693 Evaluate side-chains 56 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 46 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.082520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.064490 restraints weight = 12018.156| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.67 r_work: 0.3007 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4150 Z= 0.131 Angle : 0.531 5.484 5638 Z= 0.280 Chirality : 0.040 0.139 682 Planarity : 0.004 0.042 689 Dihedral : 4.193 20.966 551 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.08 % Allowed : 22.45 % Favored : 73.47 % 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: 1.80 (0.38), residues: 505 helix: 2.22 (0.26), residues: 364 sheet: 0.72 (1.86), residues: 10 loop : -1.90 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 PHE 0.010 0.001 PHE Y 112 TYR 0.008 0.001 TYR Y 77 ARG 0.002 0.000 ARG E 13 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 287) hydrogen bonds : angle 3.75853 ( 861) covalent geometry : bond 0.00292 ( 4150) covalent geometry : angle 0.53058 ( 5638) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.486 Fit side-chains REVERT: Y 90 ASP cc_start: 0.8197 (m-30) cc_final: 0.7808 (t0) REVERT: Y 130 TYR cc_start: 0.8306 (t80) cc_final: 0.8032 (t80) REVERT: E 54 LEU cc_start: 0.9094 (tp) cc_final: 0.8850 (tt) REVERT: B 43 MET cc_start: 0.7586 (ptp) cc_final: 0.7344 (ptp) outliers start: 18 outliers final: 12 residues processed: 64 average time/residue: 0.1332 time to fit residues: 11.3263 Evaluate side-chains 58 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 46 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.081323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.063026 restraints weight = 12212.613| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.67 r_work: 0.2972 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4150 Z= 0.184 Angle : 0.578 7.104 5638 Z= 0.304 Chirality : 0.041 0.139 682 Planarity : 0.004 0.042 689 Dihedral : 4.237 22.255 551 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.54 % Allowed : 21.09 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.38), residues: 505 helix: 2.28 (0.26), residues: 363 sheet: 0.12 (1.58), residues: 14 loop : -1.90 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 98 HIS 0.003 0.001 HIS Y 424 PHE 0.011 0.001 PHE Y 112 TYR 0.008 0.001 TYR Y 359 ARG 0.002 0.000 ARG Y 366 Details of bonding type rmsd hydrogen bonds : bond 0.04710 ( 287) hydrogen bonds : angle 3.87572 ( 861) covalent geometry : bond 0.00426 ( 4150) covalent geometry : angle 0.57764 ( 5638) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.451 Fit side-chains REVERT: Y 90 ASP cc_start: 0.8216 (m-30) cc_final: 0.7856 (t0) REVERT: Y 130 TYR cc_start: 0.8329 (t80) cc_final: 0.8057 (t80) REVERT: Y 336 MET cc_start: 0.8787 (ttm) cc_final: 0.8278 (tpt) REVERT: E 54 LEU cc_start: 0.9084 (tp) cc_final: 0.8854 (tt) REVERT: B 43 MET cc_start: 0.7661 (ptp) cc_final: 0.7340 (ptp) outliers start: 20 outliers final: 16 residues processed: 58 average time/residue: 0.1243 time to fit residues: 9.8167 Evaluate side-chains 60 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 32 THR Chi-restraints excluded: chain Y residue 139 MET Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.0770 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.082887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.064821 restraints weight = 11968.259| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.67 r_work: 0.3013 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4150 Z= 0.121 Angle : 0.513 6.176 5638 Z= 0.271 Chirality : 0.040 0.140 682 Planarity : 0.004 0.041 689 Dihedral : 4.094 19.902 551 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.72 % Allowed : 22.45 % Favored : 74.83 % 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: 2.17 (0.38), residues: 505 helix: 2.49 (0.26), residues: 365 sheet: 0.46 (1.57), residues: 14 loop : -1.77 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 PHE 0.010 0.001 PHE E 43 TYR 0.008 0.001 TYR Y 77 ARG 0.001 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 287) hydrogen bonds : angle 3.69808 ( 861) covalent geometry : bond 0.00265 ( 4150) covalent geometry : angle 0.51343 ( 5638) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.486 Fit side-chains REVERT: Y 90 ASP cc_start: 0.8119 (m-30) cc_final: 0.7853 (t0) REVERT: Y 130 TYR cc_start: 0.8296 (t80) cc_final: 0.7993 (t80) REVERT: Y 336 MET cc_start: 0.8700 (ttm) cc_final: 0.8258 (tpt) REVERT: E 14 GLU cc_start: 0.8427 (tp30) cc_final: 0.8063 (tm-30) REVERT: E 54 LEU cc_start: 0.9089 (tp) cc_final: 0.8877 (tt) outliers start: 12 outliers final: 11 residues processed: 54 average time/residue: 0.1284 time to fit residues: 9.3555 Evaluate side-chains 55 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 0.0370 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.083111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.065149 restraints weight = 11975.093| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.66 r_work: 0.3019 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 4150 Z= 0.121 Angle : 0.515 6.442 5638 Z= 0.271 Chirality : 0.040 0.134 682 Planarity : 0.004 0.041 689 Dihedral : 4.099 21.116 551 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.17 % Allowed : 22.68 % Favored : 74.15 % 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: 2.44 (0.38), residues: 505 helix: 2.73 (0.26), residues: 358 sheet: 0.53 (1.55), residues: 14 loop : -1.60 (0.55), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 98 HIS 0.001 0.000 HIS B 42 PHE 0.008 0.001 PHE Y 112 TYR 0.014 0.001 TYR Y 326 ARG 0.001 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 287) hydrogen bonds : angle 3.68828 ( 861) covalent geometry : bond 0.00265 ( 4150) covalent geometry : angle 0.51509 ( 5638) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.482 Fit side-chains REVERT: Y 90 ASP cc_start: 0.8046 (m-30) cc_final: 0.7797 (t0) REVERT: Y 130 TYR cc_start: 0.8304 (t80) cc_final: 0.8002 (t80) REVERT: Y 173 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8382 (mttp) REVERT: Y 336 MET cc_start: 0.8686 (ttm) cc_final: 0.8270 (tpt) REVERT: E 14 GLU cc_start: 0.8393 (tp30) cc_final: 0.8078 (tm-30) REVERT: E 54 LEU cc_start: 0.9097 (tp) cc_final: 0.8885 (tt) outliers start: 14 outliers final: 14 residues processed: 58 average time/residue: 0.1412 time to fit residues: 10.7571 Evaluate side-chains 60 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 46 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 48 optimal weight: 0.0570 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.083710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.065732 restraints weight = 11866.717| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.66 r_work: 0.3032 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4150 Z= 0.120 Angle : 0.538 7.188 5638 Z= 0.279 Chirality : 0.040 0.133 682 Planarity : 0.004 0.042 689 Dihedral : 3.979 19.323 551 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.17 % Allowed : 23.81 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.38), residues: 505 helix: 2.64 (0.26), residues: 365 sheet: 0.61 (1.54), residues: 14 loop : -1.53 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 PHE 0.008 0.001 PHE Y 184 TYR 0.013 0.001 TYR Y 326 ARG 0.001 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 287) hydrogen bonds : angle 3.61481 ( 861) covalent geometry : bond 0.00266 ( 4150) covalent geometry : angle 0.53846 ( 5638) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.488 Fit side-chains REVERT: Y 90 ASP cc_start: 0.7980 (m-30) cc_final: 0.7716 (t0) REVERT: Y 130 TYR cc_start: 0.8310 (t80) cc_final: 0.8008 (t80) REVERT: Y 173 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8430 (mttp) REVERT: Y 336 MET cc_start: 0.8694 (ttm) cc_final: 0.8349 (tpt) REVERT: E 14 GLU cc_start: 0.8371 (tp30) cc_final: 0.8097 (tm-30) REVERT: E 54 LEU cc_start: 0.9107 (tp) cc_final: 0.8905 (tt) REVERT: E 56 ARG cc_start: 0.8465 (ptm-80) cc_final: 0.8259 (ppt170) outliers start: 14 outliers final: 11 residues processed: 59 average time/residue: 0.1407 time to fit residues: 10.9276 Evaluate side-chains 58 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.081797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.063430 restraints weight = 12083.351| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.67 r_work: 0.2983 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4150 Z= 0.165 Angle : 0.590 12.880 5638 Z= 0.307 Chirality : 0.041 0.131 682 Planarity : 0.004 0.042 689 Dihedral : 3.992 21.416 551 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.72 % Allowed : 24.26 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.38), residues: 505 helix: 2.59 (0.26), residues: 365 sheet: 0.63 (1.55), residues: 14 loop : -1.55 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 98 HIS 0.002 0.001 HIS Y 424 PHE 0.028 0.001 PHE E 43 TYR 0.017 0.001 TYR Y 326 ARG 0.001 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 287) hydrogen bonds : angle 3.76054 ( 861) covalent geometry : bond 0.00384 ( 4150) covalent geometry : angle 0.59038 ( 5638) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.551 Fit side-chains REVERT: Y 90 ASP cc_start: 0.8050 (m-30) cc_final: 0.7796 (t0) REVERT: Y 130 TYR cc_start: 0.8310 (t80) cc_final: 0.8023 (t80) REVERT: Y 173 LYS cc_start: 0.8667 (mtmt) cc_final: 0.8374 (mttp) REVERT: Y 336 MET cc_start: 0.8712 (ttm) cc_final: 0.8277 (tpt) REVERT: E 14 GLU cc_start: 0.8422 (tp30) cc_final: 0.8124 (tm-30) REVERT: E 54 LEU cc_start: 0.9083 (tp) cc_final: 0.8863 (tt) outliers start: 12 outliers final: 11 residues processed: 53 average time/residue: 0.2604 time to fit residues: 18.1021 Evaluate side-chains 56 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain Y residue 429 ILE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 0.0030 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.0010 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.083941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.065988 restraints weight = 11935.669| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.67 r_work: 0.3041 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4150 Z= 0.116 Angle : 0.560 14.311 5638 Z= 0.285 Chirality : 0.039 0.132 682 Planarity : 0.004 0.041 689 Dihedral : 3.866 17.772 551 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.27 % Allowed : 24.94 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.38), residues: 505 helix: 2.74 (0.26), residues: 364 sheet: 0.68 (1.52), residues: 14 loop : -1.33 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Y 98 HIS 0.003 0.001 HIS B 42 PHE 0.025 0.001 PHE E 43 TYR 0.013 0.001 TYR Y 326 ARG 0.001 0.000 ARG E 56 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 287) hydrogen bonds : angle 3.56930 ( 861) covalent geometry : bond 0.00250 ( 4150) covalent geometry : angle 0.56003 ( 5638) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1010 Ramachandran restraints generated. 505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.483 Fit side-chains REVERT: Y 90 ASP cc_start: 0.7997 (m-30) cc_final: 0.7761 (t0) REVERT: Y 130 TYR cc_start: 0.8313 (t80) cc_final: 0.8031 (t80) REVERT: Y 173 LYS cc_start: 0.8665 (mtmt) cc_final: 0.8420 (mttp) REVERT: Y 336 MET cc_start: 0.8685 (ttm) cc_final: 0.8350 (tpt) REVERT: E 14 GLU cc_start: 0.8360 (tp30) cc_final: 0.8106 (tm-30) REVERT: E 54 LEU cc_start: 0.9105 (tp) cc_final: 0.8900 (tt) REVERT: E 56 ARG cc_start: 0.8440 (ptm-80) cc_final: 0.8221 (ppt170) REVERT: B 48 PHE cc_start: 0.7554 (t80) cc_final: 0.7004 (t80) REVERT: B 49 LEU cc_start: 0.9127 (mt) cc_final: 0.8769 (mm) outliers start: 10 outliers final: 10 residues processed: 57 average time/residue: 0.1437 time to fit residues: 10.7553 Evaluate side-chains 58 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 154 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 418 SER Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.083413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.065297 restraints weight = 12011.201| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.68 r_work: 0.3023 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4150 Z= 0.133 Angle : 0.583 13.785 5638 Z= 0.297 Chirality : 0.040 0.130 682 Planarity : 0.004 0.042 689 Dihedral : 3.855 19.629 551 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.49 % Allowed : 24.94 % Favored : 72.56 % 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 (0.38), residues: 505 helix: 2.78 (0.26), residues: 365 sheet: 0.67 (1.53), residues: 14 loop : -1.41 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 PHE 0.026 0.001 PHE E 43 TYR 0.014 0.001 TYR Y 326 ARG 0.001 0.000 ARG Y 423 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 287) hydrogen bonds : angle 3.60496 ( 861) covalent geometry : bond 0.00306 ( 4150) covalent geometry : angle 0.58295 ( 5638) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.03 seconds wall clock time: 40 minutes 7.64 seconds (2407.64 seconds total)