Starting phenix.real_space_refine on Wed Sep 17 04:24:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ya3_39090/09_2025/8ya3_39090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ya3_39090/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ya3_39090/09_2025/8ya3_39090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ya3_39090/09_2025/8ya3_39090.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ya3_39090/09_2025/8ya3_39090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ya3_39090/09_2025/8ya3_39090.map" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.05, per 1000 atoms: 0.26 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: 0.27 Conformation dependent library (CDL) restraints added in 163.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.12 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: 0.57 Time building geometry restraints manager: 0.40 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.860 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.290 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG Y 366 TYR 0.013 0.002 TYR Y 326 PHE 0.019 0.002 PHE Y 328 TRP 0.017 0.003 TRP Y 98 HIS 0.004 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00898 ( 4150) covalent geometry : angle 0.93317 ( 5638) hydrogen bonds : bond 0.11954 ( 287) hydrogen bonds : angle 5.69910 ( 861) *********************** 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 : 0.129 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: 0.1035 time to fit residues: 7.2144 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 : 0.150 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 85 GLN Y 235 GLN Y 267 ASN Y 387 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.081894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063725 restraints weight = 12107.742| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.74 r_work: 0.2993 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4150 Z= 0.126 Angle : 0.559 5.438 5638 Z= 0.299 Chirality : 0.040 0.150 682 Planarity : 0.005 0.048 689 Dihedral : 5.076 39.646 553 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.27 % Allowed : 21.54 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.36), residues: 505 helix: 0.94 (0.25), residues: 365 sheet: 0.31 (1.80), residues: 10 loop : -2.42 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 423 TYR 0.008 0.001 TYR Y 359 PHE 0.015 0.001 PHE Y 291 TRP 0.009 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 4150) covalent geometry : angle 0.55854 ( 5638) hydrogen bonds : bond 0.04881 ( 287) hydrogen bonds : angle 4.11686 ( 861) *********************** 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 : 0.162 Fit side-chains revert: symmetry clash REVERT: Y 250 GLU cc_start: 0.8023 (tt0) cc_final: 0.7739 (tm-30) REVERT: E 54 LEU cc_start: 0.9016 (tp) cc_final: 0.8787 (tt) REVERT: B 40 THR cc_start: 0.7992 (t) cc_final: 0.7517 (t) REVERT: B 43 MET cc_start: 0.7689 (ptp) cc_final: 0.7190 (ptp) outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 0.0700 time to fit residues: 5.5275 Evaluate side-chains 54 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 312 MET Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain E residue 49 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 18 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.082921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.065061 restraints weight = 11984.986| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.66 r_work: 0.3025 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2044 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= 0.118 Angle : 0.514 5.434 5638 Z= 0.271 Chirality : 0.040 0.145 682 Planarity : 0.004 0.044 689 Dihedral : 4.598 38.887 553 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.04 % Allowed : 24.04 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.38), residues: 505 helix: 1.87 (0.26), residues: 365 sheet: 0.64 (1.87), residues: 10 loop : -2.06 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 302 TYR 0.007 0.001 TYR Y 77 PHE 0.011 0.001 PHE Y 291 TRP 0.009 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 4150) covalent geometry : angle 0.51363 ( 5638) hydrogen bonds : bond 0.04305 ( 287) hydrogen bonds : angle 3.77975 ( 861) *********************** 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 62 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.163 Fit side-chains REVERT: Y 90 ASP cc_start: 0.8197 (m-30) cc_final: 0.7800 (t0) REVERT: Y 130 TYR cc_start: 0.8288 (t80) cc_final: 0.8024 (t80) REVERT: E 10 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8636 (mm-30) REVERT: E 54 LEU cc_start: 0.9081 (tp) cc_final: 0.8855 (tt) REVERT: B 43 MET cc_start: 0.7624 (ptp) cc_final: 0.7382 (ptp) outliers start: 9 outliers final: 5 residues processed: 59 average time/residue: 0.0623 time to fit residues: 4.8115 Evaluate side-chains 52 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 17 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 43 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.083195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065094 restraints weight = 11931.228| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.69 r_work: 0.3019 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2305 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= 0.125 Angle : 0.517 5.466 5638 Z= 0.272 Chirality : 0.040 0.138 682 Planarity : 0.004 0.042 689 Dihedral : 4.136 20.745 551 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.17 % Allowed : 22.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.38), residues: 505 helix: 2.23 (0.26), residues: 364 sheet: 0.79 (1.84), residues: 10 loop : -1.87 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 366 TYR 0.008 0.001 TYR Y 77 PHE 0.010 0.001 PHE Y 112 TRP 0.008 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4150) covalent geometry : angle 0.51685 ( 5638) hydrogen bonds : bond 0.04261 ( 287) hydrogen bonds : angle 3.72012 ( 861) *********************** 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 63 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.137 Fit side-chains REVERT: Y 90 ASP cc_start: 0.8192 (m-30) cc_final: 0.7802 (t0) REVERT: Y 130 TYR cc_start: 0.8294 (t80) cc_final: 0.8003 (t80) REVERT: Y 173 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8403 (mttp) REVERT: E 10 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8851 (mm-30) REVERT: E 54 LEU cc_start: 0.9085 (tp) cc_final: 0.8867 (tt) REVERT: B 48 PHE cc_start: 0.7750 (t80) cc_final: 0.7239 (t80) outliers start: 14 outliers final: 10 residues processed: 59 average time/residue: 0.0607 time to fit residues: 4.6358 Evaluate side-chains 55 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 0.0870 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.0960 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.082318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.064036 restraints weight = 11975.972| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.73 r_work: 0.2992 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4150 Z= 0.151 Angle : 0.542 5.875 5638 Z= 0.285 Chirality : 0.040 0.135 682 Planarity : 0.004 0.042 689 Dihedral : 4.154 21.535 551 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.31 % Allowed : 20.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.38), residues: 505 helix: 2.50 (0.26), residues: 358 sheet: 0.91 (1.86), residues: 10 loop : -1.69 (0.54), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 366 TYR 0.008 0.001 TYR Y 77 PHE 0.010 0.001 PHE Y 112 TRP 0.008 0.001 TRP Y 98 HIS 0.002 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4150) covalent geometry : angle 0.54200 ( 5638) hydrogen bonds : bond 0.04460 ( 287) hydrogen bonds : angle 3.76232 ( 861) *********************** 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 67 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.165 Fit side-chains REVERT: Y 90 ASP cc_start: 0.8154 (m-30) cc_final: 0.7852 (t0) REVERT: Y 130 TYR cc_start: 0.8314 (t80) cc_final: 0.8031 (t80) REVERT: Y 173 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8422 (mttp) REVERT: Y 336 MET cc_start: 0.9012 (ttm) cc_final: 0.8288 (tpt) REVERT: E 10 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8854 (mm-30) REVERT: E 14 GLU cc_start: 0.8455 (tp30) cc_final: 0.8036 (tm-30) REVERT: E 54 LEU cc_start: 0.9084 (tp) cc_final: 0.8863 (tt) REVERT: B 48 PHE cc_start: 0.7833 (t80) cc_final: 0.7295 (t80) outliers start: 19 outliers final: 13 residues processed: 60 average time/residue: 0.0534 time to fit residues: 4.2908 Evaluate side-chains 59 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.082773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.064679 restraints weight = 12134.932| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.67 r_work: 0.3012 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2423 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= 0.134 Angle : 0.526 6.019 5638 Z= 0.276 Chirality : 0.040 0.135 682 Planarity : 0.004 0.042 689 Dihedral : 4.115 20.798 551 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.40 % Allowed : 21.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.38), residues: 505 helix: 2.63 (0.26), residues: 359 sheet: 0.35 (1.55), residues: 14 loop : -1.66 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 366 TYR 0.007 0.001 TYR Y 359 PHE 0.009 0.001 PHE Y 112 TRP 0.007 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4150) covalent geometry : angle 0.52552 ( 5638) hydrogen bonds : bond 0.04348 ( 287) hydrogen bonds : angle 3.70906 ( 861) *********************** 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 64 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.135 Fit side-chains REVERT: Y 90 ASP cc_start: 0.8151 (m-30) cc_final: 0.7822 (t0) REVERT: Y 130 TYR cc_start: 0.8325 (t80) cc_final: 0.8025 (t80) REVERT: Y 173 LYS cc_start: 0.8680 (mtmt) cc_final: 0.8416 (mttp) REVERT: Y 336 MET cc_start: 0.8975 (ttm) cc_final: 0.8269 (tpt) REVERT: E 14 GLU cc_start: 0.8367 (tp30) cc_final: 0.7985 (tm-30) REVERT: E 54 LEU cc_start: 0.9095 (tp) cc_final: 0.8881 (tt) REVERT: B 41 LEU cc_start: 0.8560 (mt) cc_final: 0.8313 (mt) REVERT: B 48 PHE cc_start: 0.7813 (t80) cc_final: 0.7274 (t80) outliers start: 15 outliers final: 13 residues processed: 59 average time/residue: 0.0598 time to fit residues: 4.7340 Evaluate side-chains 59 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 329 VAL Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 403 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 45 optimal weight: 0.0060 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.083089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.065071 restraints weight = 12210.853| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.69 r_work: 0.3013 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4150 Z= 0.125 Angle : 0.527 7.700 5638 Z= 0.275 Chirality : 0.040 0.132 682 Planarity : 0.004 0.042 689 Dihedral : 4.001 20.570 551 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.63 % Allowed : 22.45 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.38), residues: 505 helix: 2.73 (0.26), residues: 359 sheet: 0.48 (1.53), residues: 14 loop : -1.51 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 366 TYR 0.007 0.001 TYR Y 77 PHE 0.008 0.001 PHE Y 67 TRP 0.008 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 4150) covalent geometry : angle 0.52733 ( 5638) hydrogen bonds : bond 0.04225 ( 287) hydrogen bonds : angle 3.66483 ( 861) *********************** 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 67 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.160 Fit side-chains REVERT: Y 90 ASP cc_start: 0.8072 (m-30) cc_final: 0.7832 (t0) REVERT: Y 130 TYR cc_start: 0.8316 (t80) cc_final: 0.7984 (t80) REVERT: Y 173 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8408 (mttp) REVERT: Y 336 MET cc_start: 0.8955 (ttm) cc_final: 0.8284 (tpt) REVERT: E 14 GLU cc_start: 0.8368 (tp30) cc_final: 0.8016 (tm-30) REVERT: B 48 PHE cc_start: 0.7589 (t80) cc_final: 0.7034 (t80) REVERT: B 49 LEU cc_start: 0.9234 (mt) cc_final: 0.8788 (mm) outliers start: 16 outliers final: 15 residues processed: 62 average time/residue: 0.0571 time to fit residues: 4.7216 Evaluate side-chains 62 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.109 ------------------------------------------------------------------------------- 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 403 LEU 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 41 LEU 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 15 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 0.0060 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 chunk 48 optimal weight: 0.3980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.084046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.066310 restraints weight = 11846.562| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.66 r_work: 0.3046 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4150 Z= 0.116 Angle : 0.525 6.860 5638 Z= 0.273 Chirality : 0.040 0.132 682 Planarity : 0.004 0.041 689 Dihedral : 4.061 24.438 551 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.72 % Allowed : 23.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.62 (0.39), residues: 505 helix: 2.81 (0.26), residues: 359 sheet: 0.47 (1.55), residues: 14 loop : -1.36 (0.57), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Y 366 TYR 0.007 0.001 TYR Y 233 PHE 0.009 0.001 PHE Y 67 TRP 0.007 0.001 TRP Y 98 HIS 0.001 0.000 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 4150) covalent geometry : angle 0.52536 ( 5638) hydrogen bonds : bond 0.04066 ( 287) hydrogen bonds : angle 3.61788 ( 861) *********************** 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 60 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.140 Fit side-chains REVERT: Y 90 ASP cc_start: 0.7988 (m-30) cc_final: 0.7719 (t0) REVERT: Y 130 TYR cc_start: 0.8286 (t80) cc_final: 0.7945 (t80) REVERT: Y 173 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8424 (mttp) REVERT: Y 336 MET cc_start: 0.8950 (ttm) cc_final: 0.8290 (tpt) REVERT: E 14 GLU cc_start: 0.8363 (tp30) cc_final: 0.8036 (tm-30) REVERT: B 48 PHE cc_start: 0.7704 (t80) cc_final: 0.7137 (t80) REVERT: B 49 LEU cc_start: 0.9164 (mt) cc_final: 0.8743 (mm) outliers start: 12 outliers final: 11 residues processed: 55 average time/residue: 0.0486 time to fit residues: 3.6666 Evaluate side-chains 57 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Y residue 385 PHE Chi-restraints excluded: chain Y residue 403 LEU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.083303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.065217 restraints weight = 12286.767| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.71 r_work: 0.3023 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4150 Z= 0.130 Angle : 0.544 8.158 5638 Z= 0.282 Chirality : 0.040 0.129 682 Planarity : 0.004 0.042 689 Dihedral : 3.979 24.251 551 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.17 % Allowed : 22.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.39), residues: 505 helix: 2.86 (0.26), residues: 359 sheet: 0.60 (1.53), residues: 14 loop : -1.24 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 366 TYR 0.007 0.001 TYR Y 77 PHE 0.029 0.001 PHE E 43 TRP 0.008 0.001 TRP Y 98 HIS 0.001 0.000 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4150) covalent geometry : angle 0.54378 ( 5638) hydrogen bonds : bond 0.04188 ( 287) hydrogen bonds : angle 3.69750 ( 861) *********************** 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 62 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.165 Fit side-chains REVERT: Y 24 MET cc_start: 0.9226 (mmp) cc_final: 0.9008 (mmp) REVERT: Y 90 ASP cc_start: 0.7975 (m-30) cc_final: 0.7732 (t0) REVERT: Y 130 TYR cc_start: 0.8272 (t80) cc_final: 0.7923 (t80) REVERT: Y 173 LYS cc_start: 0.8669 (mtmt) cc_final: 0.8415 (mttp) REVERT: Y 336 MET cc_start: 0.8944 (ttm) cc_final: 0.8286 (tpt) REVERT: E 14 GLU cc_start: 0.8354 (tp30) cc_final: 0.8053 (tm-30) REVERT: B 48 PHE cc_start: 0.7603 (t80) cc_final: 0.6971 (t80) REVERT: B 49 LEU cc_start: 0.9114 (mt) cc_final: 0.8712 (mm) outliers start: 14 outliers final: 12 residues processed: 56 average time/residue: 0.0502 time to fit residues: 3.9362 Evaluate side-chains 59 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 403 LEU 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 46 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.083981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.066013 restraints weight = 11975.084| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.72 r_work: 0.3039 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4150 Z= 0.119 Angle : 0.530 7.868 5638 Z= 0.273 Chirality : 0.040 0.129 682 Planarity : 0.004 0.041 689 Dihedral : 3.954 25.894 551 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.49 % Allowed : 23.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.82 (0.38), residues: 505 helix: 2.89 (0.26), residues: 358 sheet: 1.04 (1.53), residues: 14 loop : -1.08 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 366 TYR 0.007 0.001 TYR Y 233 PHE 0.026 0.001 PHE E 43 TRP 0.007 0.001 TRP Y 98 HIS 0.001 0.000 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4150) covalent geometry : angle 0.52985 ( 5638) hydrogen bonds : bond 0.04036 ( 287) hydrogen bonds : angle 3.63570 ( 861) ********************** 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: 11 poor density : 49 time to evaluate : 0.115 Fit side-chains REVERT: Y 130 TYR cc_start: 0.8293 (t80) cc_final: 0.7963 (t80) REVERT: Y 173 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8389 (mttp) REVERT: Y 336 MET cc_start: 0.8943 (ttm) cc_final: 0.8297 (tpt) REVERT: E 14 GLU cc_start: 0.8313 (tp30) cc_final: 0.8032 (tm-30) REVERT: B 48 PHE cc_start: 0.7566 (t80) cc_final: 0.6933 (t80) REVERT: B 49 LEU cc_start: 0.9139 (mt) cc_final: 0.8780 (mm) outliers start: 11 outliers final: 11 residues processed: 55 average time/residue: 0.0452 time to fit residues: 3.3950 Evaluate side-chains 60 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 403 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.083599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.065494 restraints weight = 12098.922| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.77 r_work: 0.3022 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4150 Z= 0.130 Angle : 0.551 8.129 5638 Z= 0.286 Chirality : 0.040 0.130 682 Planarity : 0.004 0.042 689 Dihedral : 3.932 25.282 551 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.95 % Allowed : 23.81 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.83 (0.38), residues: 505 helix: 2.90 (0.26), residues: 358 sheet: 0.98 (1.50), residues: 14 loop : -1.04 (0.57), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 366 TYR 0.007 0.001 TYR Y 233 PHE 0.026 0.001 PHE E 43 TRP 0.008 0.001 TRP Y 98 HIS 0.001 0.000 HIS Y 424 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4150) covalent geometry : angle 0.55124 ( 5638) hydrogen bonds : bond 0.04135 ( 287) hydrogen bonds : angle 3.66338 ( 861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1073.08 seconds wall clock time: 19 minutes 6.12 seconds (1146.12 seconds total)