Starting phenix.real_space_refine on Wed Mar 5 23:14:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zz4_15034/03_2025/7zz4_15034.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz4_15034/03_2025/7zz4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zz4_15034/03_2025/7zz4_15034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz4_15034/03_2025/7zz4_15034.map" model { file = "/net/cci-nas-00/data/ceres_data/7zz4_15034/03_2025/7zz4_15034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz4_15034/03_2025/7zz4_15034.cif" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.45, per 1000 atoms: 0.94 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: 0.91 Conformation dependent library (CDL) restraints added in 400.9 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: 0.62 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: 1.16 Time building geometry restraints manager: 1.10 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: 2.730 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.540 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:14.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.030 ------------------------------------------------------------------------------- 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= 0.506 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (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 HIS 0.005 0.001 HIS A 222 PHE 0.031 0.003 PHE A 396 TYR 0.012 0.002 TYR A 82 ARG 0.008 0.001 ARG A 458 *********************** 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 : 0.405 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 1.2960 time to fit residues: 27.1854 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 : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 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 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.065369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.058463 restraints weight = 14408.230| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.66 r_work: 0.3220 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1073 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= 0.241 Angle : 0.570 6.078 5078 Z= 0.309 Chirality : 0.044 0.183 559 Planarity : 0.003 0.023 660 Dihedral : 12.630 82.239 592 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.59 % Allowed : 18.57 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.39), residues: 461 helix: 1.16 (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 HIS 0.005 0.001 HIS A 222 PHE 0.011 0.002 PHE A 396 TYR 0.010 0.001 TYR A 48 ARG 0.003 0.000 ARG A 458 *********************** 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 : 0.423 Fit side-chains revert: symmetry clash REVERT: A 168 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7160 (ttp80) outliers start: 6 outliers final: 2 residues processed: 24 average time/residue: 1.2632 time to fit residues: 31.7430 Evaluate side-chains 19 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU 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 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 13 optimal weight: 0.0470 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.065636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.058740 restraints weight = 14445.992| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.65 r_work: 0.3224 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3743 Z= 0.202 Angle : 0.515 5.330 5078 Z= 0.281 Chirality : 0.043 0.187 559 Planarity : 0.003 0.020 660 Dihedral : 12.277 89.771 592 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.39), residues: 461 helix: 1.49 (0.38), residues: 192 sheet: 0.72 (0.55), residues: 91 loop : -1.12 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.014 0.001 PHE A 414 TYR 0.009 0.001 TYR A 82 ARG 0.007 0.000 ARG A 458 *********************** 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 27 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.624 Fit side-chains REVERT: A 168 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7379 (mtp85) REVERT: A 226 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8609 (mtm-85) REVERT: A 420 LYS cc_start: 0.6292 (tptt) cc_final: 0.5984 (tptt) REVERT: A 458 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.7834 (mtm-85) outliers start: 9 outliers final: 3 residues processed: 25 average time/residue: 1.4274 time to fit residues: 37.1202 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 : 0.434 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.0060 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.065333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.058545 restraints weight = 14690.563| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.67 r_work: 0.3221 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1390 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= 0.210 Angle : 0.530 6.395 5078 Z= 0.287 Chirality : 0.044 0.186 559 Planarity : 0.003 0.019 660 Dihedral : 11.996 83.629 592 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.58 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.39), residues: 461 helix: 1.63 (0.38), residues: 192 sheet: 0.86 (0.55), residues: 91 loop : -1.08 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 108 PHE 0.015 0.001 PHE A 414 TYR 0.009 0.001 TYR A 82 ARG 0.004 0.000 ARG A 458 *********************** 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 : 0.427 Fit side-chains REVERT: A 1 MET cc_start: 0.8585 (ptp) cc_final: 0.8246 (ptp) REVERT: A 168 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7226 (mtp85) REVERT: A 226 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8711 (mtm-85) outliers start: 6 outliers final: 3 residues processed: 24 average time/residue: 1.4623 time to fit residues: 36.4675 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 : 0.416 ------------------------------------------------------------------------------- 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 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.0970 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.065680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.058791 restraints weight = 14619.906| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.67 r_work: 0.3225 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1485 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= 0.204 Angle : 0.520 5.790 5078 Z= 0.281 Chirality : 0.043 0.186 559 Planarity : 0.003 0.021 660 Dihedral : 11.857 82.752 592 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.59 % Allowed : 19.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.39), residues: 461 helix: 1.68 (0.38), residues: 192 sheet: 0.88 (0.55), residues: 91 loop : -1.03 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.017 0.001 PHE A 414 TYR 0.009 0.001 TYR A 82 ARG 0.010 0.000 ARG A 458 *********************** 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 20 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 14 time to evaluate : 0.465 Fit side-chains REVERT: A 168 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7137 (mtp85) REVERT: A 226 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8710 (mtm-85) outliers start: 6 outliers final: 3 residues processed: 19 average time/residue: 1.0324 time to fit residues: 20.8223 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 : 0.426 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.064912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.058078 restraints weight = 14531.227| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.65 r_work: 0.3208 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3743 Z= 0.243 Angle : 0.529 5.285 5078 Z= 0.286 Chirality : 0.044 0.185 559 Planarity : 0.003 0.020 660 Dihedral : 11.893 82.785 592 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.39), residues: 461 helix: 1.70 (0.38), residues: 192 sheet: 0.90 (0.55), residues: 91 loop : -1.05 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.018 0.002 PHE A 414 TYR 0.011 0.001 TYR A 82 ARG 0.008 0.000 ARG A 458 *********************** 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 25 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 16 time to evaluate : 0.406 Fit side-chains REVERT: A 1 MET cc_start: 0.8625 (ptp) cc_final: 0.8272 (ptp) REVERT: A 168 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7264 (mtp85) REVERT: A 226 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8824 (mtm-85) REVERT: A 458 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.7791 (mtm-85) outliers start: 9 outliers final: 4 residues processed: 23 average time/residue: 1.2760 time to fit residues: 30.7495 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 : 0.407 ------------------------------------------------------------------------------- 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 15 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.065281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.058464 restraints weight = 14489.111| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.65 r_work: 0.3219 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1582 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= 0.205 Angle : 0.516 5.056 5078 Z= 0.279 Chirality : 0.044 0.186 559 Planarity : 0.003 0.018 660 Dihedral : 11.775 83.497 592 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.39 % Allowed : 18.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.39), residues: 461 helix: 1.77 (0.38), residues: 192 sheet: 0.92 (0.55), residues: 91 loop : -1.00 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.016 0.001 PHE A 414 TYR 0.009 0.001 TYR A 82 ARG 0.007 0.000 ARG A 458 *********************** 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 25 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 16 time to evaluate : 0.396 Fit side-chains REVERT: A 1 MET cc_start: 0.8625 (ptp) cc_final: 0.8236 (ptp) REVERT: A 168 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7231 (mtp85) REVERT: A 226 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8806 (mtm-85) REVERT: A 414 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8212 (t80) REVERT: A 458 ARG cc_start: 0.8367 (mtm-85) cc_final: 0.7798 (mtm-85) outliers start: 9 outliers final: 3 residues processed: 23 average time/residue: 1.1264 time to fit residues: 27.4047 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 : 0.427 ------------------------------------------------------------------------------- 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: 0.0980 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.065660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.058979 restraints weight = 14722.734| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.66 r_work: 0.3232 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3743 Z= 0.161 Angle : 0.493 4.828 5078 Z= 0.266 Chirality : 0.043 0.186 559 Planarity : 0.003 0.020 660 Dihedral : 11.413 88.119 592 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.12 % Allowed : 18.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.40), residues: 461 helix: 1.91 (0.39), residues: 192 sheet: 0.98 (0.55), residues: 91 loop : -0.92 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 222 PHE 0.013 0.001 PHE A 414 TYR 0.007 0.001 TYR A 82 ARG 0.007 0.000 ARG A 458 *********************** 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 30 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.421 Fit side-chains REVERT: A 1 MET cc_start: 0.8632 (ptp) cc_final: 0.8239 (ptp) REVERT: A 226 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8697 (mtm-85) REVERT: A 458 ARG cc_start: 0.8329 (mtm-85) cc_final: 0.7742 (mtm-85) outliers start: 8 outliers final: 3 residues processed: 27 average time/residue: 1.1544 time to fit residues: 32.6343 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 : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 391 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 45 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.064890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.058066 restraints weight = 14357.220| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.61 r_work: 0.3212 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3743 Z= 0.243 Angle : 0.547 6.073 5078 Z= 0.296 Chirality : 0.044 0.186 559 Planarity : 0.003 0.026 660 Dihedral : 11.632 89.211 592 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.86 % Allowed : 19.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.39), residues: 461 helix: 1.82 (0.38), residues: 192 sheet: 0.99 (0.56), residues: 91 loop : -0.91 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.022 0.002 PHE A 414 TYR 0.011 0.001 TYR A 82 ARG 0.006 0.000 ARG A 458 *********************** 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 24 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 17 time to evaluate : 0.354 Fit side-chains REVERT: A 1 MET cc_start: 0.8638 (ptp) cc_final: 0.8226 (ptp) REVERT: A 226 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8819 (mtm-85) REVERT: A 458 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.7947 (mpp-170) outliers start: 7 outliers final: 4 residues processed: 22 average time/residue: 0.8364 time to fit residues: 19.6573 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 : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 2 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.0050 chunk 26 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.065611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.058692 restraints weight = 14350.608| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.64 r_work: 0.3229 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1742 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= 0.196 Angle : 0.529 5.884 5078 Z= 0.287 Chirality : 0.044 0.187 559 Planarity : 0.003 0.021 660 Dihedral : 11.455 88.133 592 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.33 % Allowed : 20.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.39), residues: 461 helix: 1.87 (0.38), residues: 192 sheet: 0.94 (0.55), residues: 91 loop : -0.88 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 222 PHE 0.016 0.001 PHE A 414 TYR 0.008 0.001 TYR A 82 ARG 0.006 0.000 ARG A 458 ********************** 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 21 residues out of total 377 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 16 time to evaluate : 0.475 Fit side-chains REVERT: A 1 MET cc_start: 0.8604 (ptp) cc_final: 0.8196 (ptp) REVERT: A 226 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8686 (mtm-85) REVERT: A 458 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.7870 (mpp-170) outliers start: 5 outliers final: 3 residues processed: 19 average time/residue: 1.0516 time to fit residues: 21.3095 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 : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 391 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 20 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 0.0050 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 overall best weight: 0.4312 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.065504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.058750 restraints weight = 14692.331| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.66 r_work: 0.3228 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1780 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= 0.183 Angle : 0.519 5.704 5078 Z= 0.281 Chirality : 0.044 0.187 559 Planarity : 0.003 0.022 660 Dihedral : 11.069 81.015 592 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.33 % Allowed : 20.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.40), residues: 461 helix: 1.90 (0.39), residues: 192 sheet: 0.96 (0.55), residues: 91 loop : -0.81 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 222 PHE 0.015 0.001 PHE A 414 TYR 0.008 0.001 TYR A 82 ARG 0.006 0.000 ARG A 458 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2419.50 seconds wall clock time: 42 minutes 27.33 seconds (2547.33 seconds total)