Starting phenix.real_space_refine on Wed Jul 1 23:16:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zz4_15034/07_2026/7zz4_15034.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz4_15034/07_2026/7zz4_15034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zz4_15034/07_2026/7zz4_15034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz4_15034/07_2026/7zz4_15034.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zz4_15034/07_2026/7zz4_15034.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zz4_15034/07_2026/7zz4_15034.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zz4_15034/07_2026/7zz4_15034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz4_15034/07_2026/7zz4_15034.map" } resolution = 2.63 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= 0.008 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 12 5.16 5 C 2305 2.51 5 N 643 2.21 5 O 715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3682 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3588 Classifications: {'peptide': 463} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 443} Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 94 Unusual residues: {' MG': 1, 'ACO': 1, 'ATP': 1} Classifications: {'undetermined': 3, 'water': 11} Link IDs: {None: 13} Time building chain proxies: 0.65, per 1000 atoms: 0.18 Number of scatterers: 3682 At special positions: 0 Unit cell: (66.78, 74.2, 71.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 P 6 15.00 Mg 1 11.99 O 715 8.00 N 643 7.00 C 2305 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: 0.33 Conformation dependent library (CDL) restraints added in 128.1 milliseconds 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 840 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 5 sheets defined 40.4% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 9 through 23 removed outlier: 3.692A pdb=" N ALA A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 removed outlier: 4.168A pdb=" N PHE A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 62 through 74 Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 106 through 115 removed outlier: 4.015A pdb=" N ASP A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 172 through 191 Processing helix chain 'A' and resid 247 through 266 Processing helix chain 'A' and resid 294 through 303 removed outlier: 4.149A pdb=" N THR A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 422 through 432 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 448 through 453 Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 removed outlier: 4.134A pdb=" N VAL A 30 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LYS A 3 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N HIS A 79 " --> pdb=" O LYS A 3 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A 5 " --> pdb=" O HIS A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 170 Processing sheet with id=AA3, first strand: chain 'A' and resid 281 through 288 removed outlier: 5.038A pdb=" N PHE A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS A 278 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE A 284 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU A 276 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 286 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N HIS A 207 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N HIS A 224 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 213 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N HIS A 222 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 229 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE A 238 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLN A 231 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS A 236 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 15.376A pdb=" N GLN A 235 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 12.220A pdb=" N THR A 343 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 237 " --> pdb=" O ARG A 341 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG A 341 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AA5, first strand: chain 'A' and resid 360 through 362 removed outlier: 4.179A pdb=" N THR A 360 " --> pdb=" O ARG A 417 " (cutoff:3.500A) 176 hydrogen bonds defined for protein. 495 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: 0.52 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 626 1.31 - 1.44: 951 1.44 - 1.56: 2136 1.56 - 1.69: 12 1.69 - 1.82: 18 Bond restraints: 3743 Sorted by residual: bond pdb=" C5A ACO A1203 " pdb=" N7A ACO A1203 " ideal model delta sigma weight residual 1.387 1.518 -0.131 1.00e-02 1.00e+04 1.72e+02 bond pdb=" C6A ACO A1203 " pdb=" N6A ACO A1203 " ideal model delta sigma weight residual 1.337 1.450 -0.113 1.00e-02 1.00e+04 1.28e+02 bond pdb=" C8A ACO A1203 " pdb=" N9A ACO A1203 " ideal model delta sigma weight residual 1.370 1.269 0.101 1.00e-02 1.00e+04 1.02e+02 bond pdb=" C5P ACO A1203 " pdb=" N4P ACO A1203 " ideal model delta sigma weight residual 1.331 1.446 -0.115 1.20e-02 6.94e+03 9.22e+01 bond pdb=" C9P ACO A1203 " pdb=" N8P ACO A1203 " ideal model delta sigma weight residual 1.333 1.453 -0.120 1.30e-02 5.92e+03 8.58e+01 ... (remaining 3738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 4997 3.34 - 6.68: 58 6.68 - 10.01: 16 10.01 - 13.35: 5 13.35 - 16.69: 2 Bond angle restraints: 5078 Sorted by residual: angle pdb=" C4A ACO A1203 " pdb=" N9A ACO A1203 " pdb=" C8A ACO A1203 " ideal model delta sigma weight residual 105.72 122.41 -16.69 1.00e+00 1.00e+00 2.78e+02 angle pdb=" P1A ACO A1203 " pdb=" O3A ACO A1203 " pdb=" P2A ACO A1203 " ideal model delta sigma weight residual 136.83 123.10 13.73 1.00e+00 1.00e+00 1.89e+02 angle pdb=" C ACO A1203 " pdb=" S1P ACO A1203 " pdb=" C2P ACO A1203 " ideal model delta sigma weight residual 101.25 112.32 -11.07 1.00e+00 1.00e+00 1.23e+02 angle pdb=" N3A ACO A1203 " pdb=" C4A ACO A1203 " pdb=" N9A ACO A1203 " ideal model delta sigma weight residual 127.04 137.63 -10.59 1.15e+00 7.59e-01 8.50e+01 angle pdb=" N7A ACO A1203 " pdb=" C8A ACO A1203 " pdb=" N9A ACO A1203 " ideal model delta sigma weight residual 114.08 105.24 8.84 1.00e+00 1.00e+00 7.81e+01 ... (remaining 5073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 1882 16.98 - 33.96: 232 33.96 - 50.94: 71 50.94 - 67.92: 15 67.92 - 84.90: 7 Dihedral angle restraints: 2207 sinusoidal: 889 harmonic: 1318 Sorted by residual: dihedral pdb=" CA ASN A 288 " pdb=" CB ASN A 288 " pdb=" CG ASN A 288 " pdb=" OD1 ASN A 288 " ideal model delta sinusoidal sigma weight residual 120.00 -168.40 -71.60 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CB GLU A 46 " pdb=" CG GLU A 46 " pdb=" CD GLU A 46 " pdb=" OE1 GLU A 46 " ideal model delta sinusoidal sigma weight residual 0.00 84.90 -84.90 1 3.00e+01 1.11e-03 9.72e+00 dihedral pdb=" CA GLU A 195 " pdb=" CB GLU A 195 " pdb=" CG GLU A 195 " pdb=" CD GLU A 195 " ideal model delta sinusoidal sigma weight residual -60.00 -118.87 58.87 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 2204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 418 0.047 - 0.093: 94 0.093 - 0.139: 41 0.139 - 0.186: 3 0.186 - 0.232: 3 Chirality restraints: 559 Sorted by residual: chirality pdb=" C3B ACO A1203 " pdb=" C2B ACO A1203 " pdb=" C4B ACO A1203 " pdb=" O3B ACO A1203 " both_signs ideal model delta sigma weight residual False -2.76 -2.53 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C2B ACO A1203 " pdb=" C1B ACO A1203 " pdb=" C3B ACO A1203 " pdb=" O2B ACO A1203 " both_signs ideal model delta sigma weight residual False -2.72 -2.49 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASP A 280 " pdb=" N ASP A 280 " pdb=" C ASP A 280 " pdb=" CB ASP A 280 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 556 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 349 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" CG ASN A 349 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 349 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 349 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 396 " -0.012 2.00e-02 2.50e+03 1.34e-02 3.14e+00 pdb=" CG PHE A 396 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 396 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 396 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 396 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 396 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 396 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 414 " -0.014 2.00e-02 2.50e+03 1.31e-02 3.01e+00 pdb=" CG PHE A 414 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 414 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 414 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 414 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 414 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 414 " -0.003 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 48 2.61 - 3.18: 3083 3.18 - 3.75: 6314 3.75 - 4.33: 8517 4.33 - 4.90: 13776 Nonbonded interactions: 31738 Sorted by model distance: nonbonded pdb=" O1G ATP A1201 " pdb="MG MG A1202 " model vdw 2.035 2.170 nonbonded pdb=" OE2 GLU A 286 " pdb="MG MG A1202 " model vdw 2.052 2.170 nonbonded pdb=" O3A ATP A1201 " pdb="MG MG A1202 " model vdw 2.068 2.170 nonbonded pdb=" O3B ATP A1201 " pdb="MG MG A1202 " model vdw 2.157 2.170 nonbonded pdb=" O1A ATP A1201 " pdb="MG MG A1202 " model vdw 2.174 2.170 ... (remaining 31733 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.320 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.008 0.131 3743 Z= 0.584 Angle : 1.052 16.688 5078 Z= 0.690 Chirality : 0.050 0.232 559 Planarity : 0.004 0.032 660 Dihedral : 17.038 84.903 1367 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.27 % Allowed : 21.22 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: -0.79 (0.37), residues: 461 helix: 0.24 (0.38), residues: 177 sheet: -0.52 (0.49), residues: 105 loop : -1.18 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 458 TYR 0.012 0.002 TYR A 82 PHE 0.031 0.003 PHE A 396 HIS 0.005 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00809 / 0.58 ( 3743) covalent geometry : angle 1.05222 / 0.69 ( 5078) hydrogen bonds : bond 0.18434 / 12.72 ( 176) hydrogen bonds : angle 7.21140 / 5.12 ( 495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 19 time to evaluate : 0.135 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.5753 time to fit residues: 11.9460 Evaluate side-chains 17 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.0060 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.065827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.058916 restraints weight = 14646.258| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.70 r_work: 0.3229 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3743 Z= 0.153 Angle : 0.565 6.330 5078 Z= 0.306 Chirality : 0.044 0.179 559 Planarity : 0.003 0.024 660 Dihedral : 7.608 66.851 520 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.59 % Allowed : 19.10 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.19 (0.39), residues: 461 helix: 1.18 (0.38), residues: 191 sheet: 0.39 (0.54), residues: 91 loop : -1.14 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 458 TYR 0.009 0.001 TYR A 48 PHE 0.011 0.001 PHE A 396 HIS 0.005 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 3743) covalent geometry : angle 0.56526 / 0.31 ( 5078) hydrogen bonds : bond 0.04291 / 2.94 ( 176) hydrogen bonds : angle 5.17043 / 3.77 ( 495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.137 Fit side-chains REVERT: A 168 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7405 (mtp85) outliers start: 6 outliers final: 1 residues processed: 23 average time/residue: 0.5772 time to fit residues: 13.7889 Evaluate side-chains 17 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 391 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 GLN A 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.064998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.058106 restraints weight = 14623.089| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.67 r_work: 0.3204 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3743 Z= 0.172 Angle : 0.536 5.432 5078 Z= 0.291 Chirality : 0.044 0.186 559 Planarity : 0.003 0.021 660 Dihedral : 7.634 68.630 520 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.39 % Allowed : 18.57 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.49 (0.39), residues: 461 helix: 1.49 (0.38), residues: 191 sheet: 0.69 (0.55), residues: 91 loop : -1.15 (0.43), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 458 TYR 0.010 0.001 TYR A 82 PHE 0.018 0.002 PHE A 414 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 3743) covalent geometry : angle 0.53641 / 0.29 ( 5078) hydrogen bonds : bond 0.04109 / 2.85 ( 176) hydrogen bonds : angle 4.88221 / 3.57 ( 495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 16 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 168 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7154 (ttp80) REVERT: A 226 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8656 (mtm-85) REVERT: A 458 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.7925 (mtm-85) outliers start: 9 outliers final: 4 residues processed: 24 average time/residue: 0.4814 time to fit residues: 12.0168 Evaluate side-chains 20 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.065817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.058966 restraints weight = 14271.104| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.63 r_work: 0.3228 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3743 Z= 0.131 Angle : 0.502 6.408 5078 Z= 0.270 Chirality : 0.043 0.188 559 Planarity : 0.003 0.019 660 Dihedral : 7.423 68.469 520 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.59 % Allowed : 18.83 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.73 (0.39), residues: 461 helix: 1.72 (0.38), residues: 192 sheet: 0.83 (0.55), residues: 91 loop : -1.09 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 458 TYR 0.008 0.001 TYR A 82 PHE 0.014 0.001 PHE A 414 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 3743) covalent geometry : angle 0.50222 / 0.27 ( 5078) hydrogen bonds : bond 0.03698 / 2.56 ( 176) hydrogen bonds : angle 4.64569 / 3.38 ( 495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8524 (ptp) cc_final: 0.8233 (ptp) REVERT: A 168 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7208 (mtp85) REVERT: A 458 ARG cc_start: 0.8284 (mtm-85) cc_final: 0.8003 (mtm-85) outliers start: 6 outliers final: 3 residues processed: 24 average time/residue: 0.5846 time to fit residues: 14.4913 Evaluate side-chains 20 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 13 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 10 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.0870 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.066499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.059750 restraints weight = 14689.035| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.67 r_work: 0.3253 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3743 Z= 0.101 Angle : 0.481 5.592 5078 Z= 0.257 Chirality : 0.043 0.184 559 Planarity : 0.003 0.022 660 Dihedral : 7.140 67.267 520 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.12 % Allowed : 18.83 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.93 (0.40), residues: 461 helix: 1.88 (0.39), residues: 192 sheet: 0.94 (0.56), residues: 91 loop : -1.00 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 458 TYR 0.007 0.001 TYR A 82 PHE 0.011 0.001 PHE A 414 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 3743) covalent geometry : angle 0.48073 / 0.26 ( 5078) hydrogen bonds : bond 0.03373 / 2.32 ( 176) hydrogen bonds : angle 4.45164 / 3.23 ( 495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: A 168 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7218 (mtp85) REVERT: A 458 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.7772 (mtm-85) outliers start: 8 outliers final: 3 residues processed: 24 average time/residue: 0.4754 time to fit residues: 11.8481 Evaluate side-chains 19 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.0770 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.065343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.058459 restraints weight = 14588.154| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.67 r_work: 0.3217 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3743 Z= 0.161 Angle : 0.513 4.975 5078 Z= 0.276 Chirality : 0.044 0.186 559 Planarity : 0.003 0.021 660 Dihedral : 7.181 69.880 520 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.65 % Allowed : 18.83 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.90 (0.39), residues: 461 helix: 1.80 (0.38), residues: 192 sheet: 1.02 (0.56), residues: 91 loop : -0.99 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 458 TYR 0.011 0.001 TYR A 82 PHE 0.018 0.002 PHE A 414 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 3743) covalent geometry : angle 0.51273 / 0.28 ( 5078) hydrogen bonds : bond 0.03696 / 2.57 ( 176) hydrogen bonds : angle 4.53521 / 3.30 ( 495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 18 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8647 (ptp) cc_final: 0.8219 (ptp) REVERT: A 168 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7276 (mtp85) outliers start: 10 outliers final: 4 residues processed: 25 average time/residue: 0.5078 time to fit residues: 13.2309 Evaluate side-chains 20 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 15 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.064880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.057998 restraints weight = 14870.650| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.68 r_work: 0.3204 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3743 Z= 0.167 Angle : 0.526 5.194 5078 Z= 0.283 Chirality : 0.044 0.186 559 Planarity : 0.003 0.020 660 Dihedral : 7.260 71.060 520 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.39 % Allowed : 18.30 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.89 (0.39), residues: 461 helix: 1.75 (0.38), residues: 192 sheet: 1.03 (0.56), residues: 91 loop : -0.95 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 458 TYR 0.011 0.001 TYR A 82 PHE 0.018 0.002 PHE A 414 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 ( 3743) covalent geometry : angle 0.52554 / 0.28 ( 5078) hydrogen bonds : bond 0.03756 / 2.61 ( 176) hydrogen bonds : angle 4.57564 / 3.33 ( 495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8679 (ptp) cc_final: 0.8293 (ptp) REVERT: A 168 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7155 (ttp80) outliers start: 9 outliers final: 3 residues processed: 24 average time/residue: 0.4008 time to fit residues: 10.1060 Evaluate side-chains 18 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 30 optimal weight: 0.0670 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.065461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.058774 restraints weight = 14933.374| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.67 r_work: 0.3226 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3743 Z= 0.115 Angle : 0.506 4.864 5078 Z= 0.275 Chirality : 0.044 0.187 559 Planarity : 0.003 0.023 660 Dihedral : 7.098 69.432 520 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.12 % Allowed : 19.36 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 1.04 (0.40), residues: 461 helix: 1.88 (0.38), residues: 192 sheet: 1.08 (0.56), residues: 91 loop : -0.86 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 458 TYR 0.008 0.001 TYR A 82 PHE 0.016 0.001 PHE A 414 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 3743) covalent geometry : angle 0.50598 / 0.28 ( 5078) hydrogen bonds : bond 0.03408 / 2.36 ( 176) hydrogen bonds : angle 4.42607 / 3.22 ( 495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.8676 (ptp) cc_final: 0.8324 (ptp) REVERT: A 168 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.7075 (ttp80) outliers start: 8 outliers final: 6 residues processed: 24 average time/residue: 0.4237 time to fit residues: 10.6226 Evaluate side-chains 21 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 14 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.064034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.057202 restraints weight = 14725.548| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.65 r_work: 0.3185 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3743 Z= 0.211 Angle : 0.569 6.045 5078 Z= 0.308 Chirality : 0.045 0.186 559 Planarity : 0.003 0.023 660 Dihedral : 7.285 73.284 520 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.12 % Allowed : 19.63 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.89 (0.39), residues: 461 helix: 1.73 (0.38), residues: 192 sheet: 0.96 (0.56), residues: 91 loop : -0.88 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 458 TYR 0.013 0.001 TYR A 82 PHE 0.025 0.002 PHE A 414 HIS 0.005 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 ( 3743) covalent geometry : angle 0.56948 / 0.31 ( 5078) hydrogen bonds : bond 0.03945 / 2.75 ( 176) hydrogen bonds : angle 4.63492 / 3.38 ( 495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 15 time to evaluate : 0.085 Fit side-chains REVERT: A 1 MET cc_start: 0.8731 (ptp) cc_final: 0.8378 (ptp) outliers start: 8 outliers final: 4 residues processed: 21 average time/residue: 0.3878 time to fit residues: 8.5356 Evaluate side-chains 17 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.065164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.058219 restraints weight = 14895.515| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.70 r_work: 0.3211 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3743 Z= 0.140 Angle : 0.563 8.361 5078 Z= 0.304 Chirality : 0.044 0.188 559 Planarity : 0.004 0.055 660 Dihedral : 7.187 72.661 520 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.33 % Allowed : 20.69 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.92 (0.39), residues: 461 helix: 1.79 (0.38), residues: 192 sheet: 0.89 (0.56), residues: 91 loop : -0.85 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 168 TYR 0.009 0.001 TYR A 82 PHE 0.017 0.001 PHE A 414 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 3743) covalent geometry : angle 0.56275 / 0.30 ( 5078) hydrogen bonds : bond 0.03674 / 2.55 ( 176) hydrogen bonds : angle 4.55973 / 3.31 ( 495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 922 Ramachandran restraints generated. 461 Oldfield, 0 Emsley, 461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.104 Fit side-chains REVERT: A 1 MET cc_start: 0.8701 (ptp) cc_final: 0.8336 (ptp) outliers start: 5 outliers final: 4 residues processed: 16 average time/residue: 0.2254 time to fit residues: 3.9805 Evaluate side-chains 18 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.064744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.057824 restraints weight = 14423.102| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.64 r_work: 0.3203 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3743 Z= 0.169 Angle : 0.570 7.954 5078 Z= 0.308 Chirality : 0.044 0.186 559 Planarity : 0.003 0.050 660 Dihedral : 7.203 74.081 520 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.33 % Allowed : 20.69 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 are not related in a simple way. whole: 0.87 (0.39), residues: 461 helix: 1.72 (0.38), residues: 192 sheet: 0.88 (0.56), residues: 91 loop : -0.85 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 168 TYR 0.011 0.001 TYR A 82 PHE 0.021 0.002 PHE A 414 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 ( 3743) covalent geometry : angle 0.57045 / 0.31 ( 5078) hydrogen bonds : bond 0.03736 / 2.60 ( 176) hydrogen bonds : angle 4.61467 / 3.35 ( 495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 980.96 seconds wall clock time: 17 minutes 34.57 seconds (1054.57 seconds total)