Starting phenix.real_space_refine on Tue Mar 3 12:15:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zz4_15034/03_2026/7zz4_15034.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz4_15034/03_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_15034/03_2026/7zz4_15034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz4_15034/03_2026/7zz4_15034.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zz4_15034/03_2026/7zz4_15034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz4_15034/03_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-5986/lib/python3.9/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: 0.96, per 1000 atoms: 0.26 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: 0.25 Conformation dependent library (CDL) restraints added in 139.1 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: 0.14 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: 0.54 Time building geometry restraints manager: 0.36 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: 1908 16.98 - 33.96: 260 33.96 - 50.94: 79 50.94 - 67.92: 23 67.92 - 84.90: 9 Dihedral angle restraints: 2279 sinusoidal: 961 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 2276 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: 1.030 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.490 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:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 18.143 84.903 1439 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 covalent geometry : bond 0.00809 ( 3743) covalent geometry : angle 1.05222 ( 5078) hydrogen bonds : bond 0.18434 ( 176) hydrogen bonds : angle 7.21140 ( 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 : 0.131 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.6290 time to fit residues: 13.0361 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 : 0.097 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.065779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.058902 restraints weight = 14558.222| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.67 r_work: 0.3230 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1050 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= 0.153 Angle : 0.558 6.019 5078 Z= 0.303 Chirality : 0.044 0.181 559 Planarity : 0.003 0.024 660 Dihedral : 12.510 81.651 592 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.86 % Allowed : 18.57 % 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: 0.21 (0.39), residues: 461 helix: 1.18 (0.38), residues: 191 sheet: 0.42 (0.54), residues: 91 loop : -1.14 (0.44), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 458 TYR 0.009 0.001 TYR A 48 PHE 0.010 0.001 PHE A 396 HIS 0.005 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3743) covalent geometry : angle 0.55813 ( 5078) hydrogen bonds : bond 0.04292 ( 176) hydrogen bonds : angle 5.09941 ( 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 26 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.139 Fit side-chains REVERT: A 168 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7377 (mtp85) outliers start: 7 outliers final: 1 residues processed: 24 average time/residue: 0.5676 time to fit residues: 14.1352 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 : 0.117 ------------------------------------------------------------------------------- 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: 0.6980 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 6 optimal weight: 0.0670 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3500 r_free = 0.3500 target = 0.065762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.058839 restraints weight = 14633.778| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.67 r_work: 0.3225 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1220 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= 0.141 Angle : 0.517 5.226 5078 Z= 0.282 Chirality : 0.043 0.188 559 Planarity : 0.003 0.020 660 Dihedral : 12.205 90.000 592 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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: 0.55 (0.39), residues: 461 helix: 1.51 (0.38), residues: 192 sheet: 0.73 (0.55), residues: 91 loop : -1.11 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 458 TYR 0.009 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 covalent geometry : bond 0.00307 ( 3743) covalent geometry : angle 0.51695 ( 5078) hydrogen bonds : bond 0.03951 ( 176) hydrogen bonds : angle 4.81878 ( 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: 8 poor density : 17 time to evaluate : 0.156 Fit side-chains REVERT: A 168 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7373 (mtp85) REVERT: A 226 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8614 (mtm-85) REVERT: A 420 LYS cc_start: 0.6290 (tptt) cc_final: 0.5987 (tptt) REVERT: A 458 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.7829 (mtm-85) outliers start: 8 outliers final: 3 residues processed: 23 average time/residue: 0.6545 time to fit residues: 15.6300 Evaluate side-chains 21 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.065007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.058266 restraints weight = 14684.106| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.65 r_work: 0.3215 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1401 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= 0.162 Angle : 0.535 6.071 5078 Z= 0.288 Chirality : 0.044 0.186 559 Planarity : 0.003 0.020 660 Dihedral : 12.014 82.579 592 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.86 % Allowed : 19.10 % 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: 0.71 (0.39), residues: 461 helix: 1.65 (0.38), residues: 192 sheet: 0.87 (0.55), residues: 91 loop : -1.08 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 458 TYR 0.010 0.001 TYR A 82 PHE 0.016 0.002 PHE A 414 HIS 0.007 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3743) covalent geometry : angle 0.53477 ( 5078) hydrogen bonds : bond 0.03938 ( 176) hydrogen bonds : angle 4.76799 ( 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 27 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.114 Fit side-chains REVERT: A 168 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7192 (mtp85) REVERT: A 226 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8719 (mtm-85) outliers start: 7 outliers final: 3 residues processed: 24 average time/residue: 0.6578 time to fit residues: 16.3230 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 : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 13 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.066285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.059414 restraints weight = 14349.797| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.65 r_work: 0.3243 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3743 Z= 0.120 Angle : 0.507 5.769 5078 Z= 0.274 Chirality : 0.043 0.186 559 Planarity : 0.003 0.028 660 Dihedral : 11.662 84.752 592 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.33 % Allowed : 19.89 % Favored : 78.78 % 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: 0.83 (0.39), residues: 461 helix: 1.75 (0.38), residues: 192 sheet: 0.92 (0.55), residues: 91 loop : -1.00 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 458 TYR 0.008 0.001 TYR A 82 PHE 0.015 0.001 PHE A 414 HIS 0.003 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3743) covalent geometry : angle 0.50742 ( 5078) hydrogen bonds : bond 0.03568 ( 176) hydrogen bonds : angle 4.57212 ( 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 21 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.150 Fit side-chains REVERT: A 1 MET cc_start: 0.8550 (ptp) cc_final: 0.8125 (ptp) REVERT: A 168 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7206 (mtp85) REVERT: A 226 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8787 (mtm-85) REVERT: A 414 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8191 (t80) outliers start: 5 outliers final: 1 residues processed: 19 average time/residue: 0.6036 time to fit residues: 12.0135 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 : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 414 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 0.0970 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.0020 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.065985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.059124 restraints weight = 14465.814| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.66 r_work: 0.3237 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 : 0.003 0.032 3743 Z= 0.126 Angle : 0.500 5.030 5078 Z= 0.270 Chirality : 0.043 0.186 559 Planarity : 0.003 0.022 660 Dihedral : 11.513 88.275 592 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.65 % Allowed : 18.57 % Favored : 78.78 % 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: 0.88 (0.39), residues: 461 helix: 1.78 (0.38), residues: 192 sheet: 0.97 (0.56), residues: 91 loop : -0.97 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 458 TYR 0.009 0.001 TYR A 82 PHE 0.015 0.001 PHE A 414 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3743) covalent geometry : angle 0.50035 ( 5078) hydrogen bonds : bond 0.03526 ( 176) hydrogen bonds : angle 4.53050 ( 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 27 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 17 time to evaluate : 0.099 Fit side-chains REVERT: A 1 MET cc_start: 0.8585 (ptp) cc_final: 0.8185 (ptp) REVERT: A 168 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7136 (mtp85) REVERT: A 226 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8795 (mtm-85) REVERT: A 414 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8184 (t80) REVERT: A 458 ARG cc_start: 0.8298 (mtm-85) cc_final: 0.7729 (mtm-85) outliers start: 10 outliers final: 3 residues processed: 25 average time/residue: 0.6198 time to fit residues: 16.0800 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 : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 391 VAL 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: 1.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 20 optimal weight: 0.0030 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.066017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.059121 restraints weight = 14670.104| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.68 r_work: 0.3235 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1598 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= 0.124 Angle : 0.512 5.253 5078 Z= 0.276 Chirality : 0.043 0.187 559 Planarity : 0.003 0.020 660 Dihedral : 11.353 87.621 592 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.86 % Allowed : 18.83 % 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: 0.94 (0.40), residues: 461 helix: 1.83 (0.38), residues: 192 sheet: 1.00 (0.56), residues: 91 loop : -0.94 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 458 TYR 0.009 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 covalent geometry : bond 0.00271 ( 3743) covalent geometry : angle 0.51214 ( 5078) hydrogen bonds : bond 0.03457 ( 176) hydrogen bonds : angle 4.48214 ( 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 23 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 16 time to evaluate : 0.142 Fit side-chains REVERT: A 1 MET cc_start: 0.8582 (ptp) cc_final: 0.8213 (ptp) REVERT: A 168 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.7175 (mtp85) REVERT: A 226 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8791 (mtm-85) REVERT: A 414 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.8172 (t80) REVERT: A 458 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.7736 (mtm-85) outliers start: 7 outliers final: 3 residues processed: 22 average time/residue: 0.5166 time to fit residues: 11.9017 Evaluate side-chains 21 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 15 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 391 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.0770 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.065517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.058635 restraints weight = 14554.015| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.66 r_work: 0.3223 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1631 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= 0.138 Angle : 0.511 4.932 5078 Z= 0.274 Chirality : 0.043 0.186 559 Planarity : 0.003 0.019 660 Dihedral : 11.262 82.702 592 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: 0.96 (0.40), residues: 461 helix: 1.84 (0.38), residues: 192 sheet: 0.99 (0.56), residues: 91 loop : -0.90 (0.44), residues: 178 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 0.015 0.001 PHE A 414 HIS 0.004 0.001 HIS A 222 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3743) covalent geometry : angle 0.51063 ( 5078) hydrogen bonds : bond 0.03540 ( 176) hydrogen bonds : angle 4.49716 ( 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 22 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.137 Fit side-chains REVERT: A 1 MET cc_start: 0.8613 (ptp) cc_final: 0.8252 (ptp) REVERT: A 168 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7088 (ttp80) REVERT: A 226 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8807 (mtm-85) REVERT: A 414 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.8208 (t80) REVERT: A 458 ARG cc_start: 0.8313 (mtm-85) cc_final: 0.7871 (mpp-170) outliers start: 6 outliers final: 3 residues processed: 21 average time/residue: 0.6680 time to fit residues: 14.5719 Evaluate side-chains 19 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 391 VAL Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 414 PHE 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: 0.8980 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 45 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.065580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.058711 restraints weight = 14485.979| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.65 r_work: 0.3229 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3743 Z= 0.133 Angle : 0.520 6.054 5078 Z= 0.282 Chirality : 0.044 0.187 559 Planarity : 0.003 0.027 660 Dihedral : 11.124 78.467 592 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.59 % Allowed : 19.36 % 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: 0.97 (0.40), residues: 461 helix: 1.86 (0.38), residues: 192 sheet: 0.95 (0.56), residues: 91 loop : -0.89 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 458 TYR 0.009 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 covalent geometry : bond 0.00291 ( 3743) covalent geometry : angle 0.51986 ( 5078) hydrogen bonds : bond 0.03481 ( 176) hydrogen bonds : angle 4.45675 ( 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 20 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.156 Fit side-chains REVERT: A 1 MET cc_start: 0.8596 (ptp) cc_final: 0.8242 (ptp) REVERT: A 168 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.7127 (ttp80) REVERT: A 226 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8691 (mtm-85) REVERT: A 414 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.8181 (t80) REVERT: A 458 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.7872 (mpp-170) outliers start: 6 outliers final: 2 residues processed: 19 average time/residue: 0.6118 time to fit residues: 12.1235 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 : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 0.0050 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.065521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.058581 restraints weight = 14810.570| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.70 r_work: 0.3224 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3743 Z= 0.132 Angle : 0.516 5.731 5078 Z= 0.279 Chirality : 0.044 0.187 559 Planarity : 0.003 0.019 660 Dihedral : 10.952 71.723 592 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.59 % Allowed : 19.36 % 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: 0.89 (0.40), residues: 461 helix: 1.90 (0.38), residues: 192 sheet: 0.44 (0.52), residues: 105 loop : -0.87 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 458 TYR 0.009 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 covalent geometry : bond 0.00289 ( 3743) covalent geometry : angle 0.51552 ( 5078) hydrogen bonds : bond 0.03455 ( 176) hydrogen bonds : angle 4.42903 ( 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 19 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.148 Fit side-chains REVERT: A 1 MET cc_start: 0.8630 (ptp) cc_final: 0.8228 (ptp) REVERT: A 168 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7091 (ttp80) REVERT: A 226 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8752 (mtm-85) REVERT: A 414 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8193 (t80) REVERT: A 458 ARG cc_start: 0.8335 (mtm-85) cc_final: 0.7885 (mpp-170) outliers start: 6 outliers final: 3 residues processed: 18 average time/residue: 0.6169 time to fit residues: 11.6004 Evaluate side-chains 19 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 13 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 35 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 0.0670 chunk 42 optimal weight: 0.0980 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.065205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.058558 restraints weight = 14538.156| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.63 r_work: 0.3225 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3743 Z= 0.123 Angle : 0.508 5.712 5078 Z= 0.274 Chirality : 0.043 0.187 559 Planarity : 0.003 0.019 660 Dihedral : 10.786 63.535 592 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.59 % Allowed : 19.36 % 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: 0.90 (0.40), residues: 461 helix: 1.91 (0.39), residues: 192 sheet: 0.41 (0.52), residues: 105 loop : -0.85 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 458 TYR 0.009 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 covalent geometry : bond 0.00270 ( 3743) covalent geometry : angle 0.50771 ( 5078) hydrogen bonds : bond 0.03405 ( 176) hydrogen bonds : angle 4.39236 ( 495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1138.65 seconds wall clock time: 20 minutes 13.84 seconds (1213.84 seconds total)