Starting phenix.real_space_refine on Tue Feb 11 01:44:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qt9_18646/02_2025/8qt9_18646.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qt9_18646/02_2025/8qt9_18646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qt9_18646/02_2025/8qt9_18646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qt9_18646/02_2025/8qt9_18646.map" model { file = "/net/cci-nas-00/data/ceres_data/8qt9_18646/02_2025/8qt9_18646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qt9_18646/02_2025/8qt9_18646.cif" } resolution = 2.36 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= 0.074 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 Fe 2 7.16 5 P 4 5.49 5 S 11 5.16 5 C 2282 2.51 5 N 555 2.21 5 O 657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3511 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3264 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 385} Chain: "A" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 247 Unusual residues: {'FAD': 1, 'HEM': 2, 'NAI': 1} Classifications: {'undetermined': 4, 'water': 64} Link IDs: {None: 67} Time building chain proxies: 3.48, per 1000 atoms: 0.99 Number of scatterers: 3511 At special positions: 0 Unit cell: (63.985, 61.12, 92.635, 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) Fe 2 26.01 S 11 16.00 P 4 15.00 O 657 8.00 N 555 7.00 C 2282 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 393.9 milliseconds 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 55.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 4 through 6 No H-bonds generated for 'chain 'A' and resid 4 through 6' Processing helix chain 'A' and resid 7 through 29 Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.559A pdb=" N THR A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 61 through 88 Processing helix chain 'A' and resid 94 through 117 removed outlier: 3.589A pdb=" N GLY A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 131 through 148 Processing helix chain 'A' and resid 155 through 178 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.596A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.554A pdb=" N SER A 301 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 372 through 387 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 195 removed outlier: 8.035A pdb=" N TYR A 186 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N GLY A 188 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER A 208 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE A 190 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N HIS A 206 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS A 192 " --> pdb=" O GLN A 204 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLN A 243 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N TYR A 246 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR A 248 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER A 236 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N LYS A 250 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE A 220 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ARG A 273 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LYS A 222 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU A 271 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE A 224 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL A 269 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 347 removed outlier: 6.550A pdb=" N VAL A 313 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N HIS A 344 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE A 315 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE A 346 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR A 317 " --> pdb=" O ILE A 346 " (cutoff:3.500A) 193 hydrogen bonds defined for protein. 555 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: 1.21 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 1429 1.38 - 1.56: 2100 1.56 - 1.73: 8 1.73 - 1.90: 21 1.90 - 2.07: 8 Bond restraints: 3566 Sorted by residual: bond pdb=" O5B FAD A 501 " pdb=" PA FAD A 501 " ideal model delta sigma weight residual 1.634 1.558 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" O5B NAI A 504 " pdb=" PA NAI A 504 " ideal model delta sigma weight residual 1.644 1.571 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" O3P FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.660 1.593 0.067 2.00e-02 2.50e+03 1.14e+01 bond pdb=" O5D NAI A 504 " pdb=" PN NAI A 504 " ideal model delta sigma weight residual 1.650 1.583 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O5' FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.637 1.570 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 3561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 4764 1.89 - 3.78: 80 3.78 - 5.66: 22 5.66 - 7.55: 6 7.55 - 9.44: 2 Bond angle restraints: 4874 Sorted by residual: angle pdb=" O1N NAI A 504 " pdb=" PN NAI A 504 " pdb=" O2N NAI A 504 " ideal model delta sigma weight residual 123.22 113.78 9.44 3.00e+00 1.11e-01 9.90e+00 angle pdb=" PA NAI A 504 " pdb=" O3 NAI A 504 " pdb=" PN NAI A 504 " ideal model delta sigma weight residual 129.27 136.82 -7.55 3.00e+00 1.11e-01 6.34e+00 angle pdb=" C GLU A 229 " pdb=" CA GLU A 229 " pdb=" CB GLU A 229 " ideal model delta sigma weight residual 109.53 113.77 -4.24 1.69e+00 3.50e-01 6.28e+00 angle pdb=" O1P FAD A 501 " pdb=" P FAD A 501 " pdb=" O2P FAD A 501 " ideal model delta sigma weight residual 122.50 115.08 7.42 3.00e+00 1.11e-01 6.12e+00 angle pdb=" C MET A 87 " pdb=" N GLY A 88 " pdb=" CA GLY A 88 " ideal model delta sigma weight residual 121.83 118.94 2.89 1.19e+00 7.06e-01 5.90e+00 ... (remaining 4869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 1724 17.78 - 35.56: 226 35.56 - 53.34: 65 53.34 - 71.13: 33 71.13 - 88.91: 15 Dihedral angle restraints: 2063 sinusoidal: 901 harmonic: 1162 Sorted by residual: dihedral pdb=" CA ASP A 261 " pdb=" CB ASP A 261 " pdb=" CG ASP A 261 " pdb=" OD1 ASP A 261 " ideal model delta sinusoidal sigma weight residual -30.00 -90.26 60.26 1 2.00e+01 2.50e-03 1.21e+01 dihedral pdb=" C1A HEM A 503 " pdb=" C2A HEM A 503 " pdb=" CAA HEM A 503 " pdb=" CBA HEM A 503 " ideal model delta sinusoidal sigma weight residual -180.00 -101.61 -78.39 2 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP A 261 " pdb=" C ASP A 261 " pdb=" N ASN A 262 " pdb=" CA ASN A 262 " ideal model delta harmonic sigma weight residual -180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 2060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 301 0.029 - 0.058: 126 0.058 - 0.086: 42 0.086 - 0.115: 28 0.115 - 0.144: 12 Chirality restraints: 509 Sorted by residual: chirality pdb=" CA THR A 297 " pdb=" N THR A 297 " pdb=" C THR A 297 " pdb=" CB THR A 297 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" C1D NAI A 504 " pdb=" C2D NAI A 504 " pdb=" N1N NAI A 504 " pdb=" O4D NAI A 504 " both_signs ideal model delta sigma weight residual False 2.29 2.43 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" C2B FAD A 501 " pdb=" C1B FAD A 501 " pdb=" C3B FAD A 501 " pdb=" O2B FAD A 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.66 0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 506 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 40 " -0.006 2.00e-02 2.50e+03 1.19e-02 1.41e+00 pdb=" C THR A 40 " 0.021 2.00e-02 2.50e+03 pdb=" O THR A 40 " -0.008 2.00e-02 2.50e+03 pdb=" N SER A 41 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 338 " -0.018 5.00e-02 4.00e+02 2.74e-02 1.20e+00 pdb=" N PRO A 339 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 45 " 0.005 2.00e-02 2.50e+03 1.06e-02 1.13e+00 pdb=" C THR A 45 " -0.018 2.00e-02 2.50e+03 pdb=" O THR A 45 " 0.007 2.00e-02 2.50e+03 pdb=" N PHE A 46 " 0.006 2.00e-02 2.50e+03 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 121 2.71 - 3.26: 3290 3.26 - 3.80: 6330 3.80 - 4.35: 8359 4.35 - 4.90: 13188 Nonbonded interactions: 31288 Sorted by model distance: nonbonded pdb=" NE2 HIS A 69 " pdb="FE HEM A 502 " model vdw 2.158 3.080 nonbonded pdb=" O HOH A 601 " pdb=" O HOH A 636 " model vdw 2.197 3.040 nonbonded pdb=" O1P FAD A 501 " pdb=" O HOH A 601 " model vdw 2.203 3.040 nonbonded pdb=" O2A FAD A 501 " pdb=" O HOH A 601 " model vdw 2.211 3.040 nonbonded pdb=" O SER A 236 " pdb=" O HOH A 602 " model vdw 2.218 3.040 ... (remaining 31283 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: 2.210 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.880 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 0.005 0.076 3566 Z= 0.313 Angle : 0.685 9.439 4874 Z= 0.314 Chirality : 0.043 0.144 509 Planarity : 0.003 0.027 579 Dihedral : 20.317 88.907 1323 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.58 % Allowed : 22.19 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.41), residues: 397 helix: 1.14 (0.36), residues: 204 sheet: 0.08 (0.52), residues: 88 loop : -0.67 (0.58), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 25 HIS 0.006 0.001 HIS A 69 PHE 0.008 0.001 PHE A 32 TYR 0.013 0.001 TYR A 144 ARG 0.001 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.353 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 1.2924 time to fit residues: 62.7776 Evaluate side-chains 47 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 93 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.130864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.114047 restraints weight = 3277.866| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.25 r_work: 0.3197 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3566 Z= 0.227 Angle : 0.660 13.547 4874 Z= 0.285 Chirality : 0.042 0.139 509 Planarity : 0.003 0.028 579 Dihedral : 12.426 85.470 564 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.59 % Allowed : 19.02 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.42), residues: 397 helix: 1.98 (0.35), residues: 204 sheet: 0.25 (0.56), residues: 82 loop : -0.04 (0.63), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 25 HIS 0.005 0.001 HIS A 69 PHE 0.008 0.001 PHE A 32 TYR 0.015 0.002 TYR A 144 ARG 0.002 0.000 ARG A 195 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.412 Fit side-chains REVERT: A 78 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7791 (mp) outliers start: 9 outliers final: 4 residues processed: 55 average time/residue: 1.0337 time to fit residues: 59.2094 Evaluate side-chains 52 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.129642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112730 restraints weight = 3279.441| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.25 r_work: 0.3180 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3566 Z= 0.263 Angle : 0.671 13.033 4874 Z= 0.295 Chirality : 0.043 0.138 509 Planarity : 0.003 0.029 579 Dihedral : 12.131 84.888 560 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.17 % Allowed : 18.73 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.42), residues: 397 helix: 1.94 (0.35), residues: 204 sheet: 0.21 (0.56), residues: 82 loop : -0.20 (0.59), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 25 HIS 0.006 0.001 HIS A 69 PHE 0.010 0.002 PHE A 224 TYR 0.017 0.002 TYR A 144 ARG 0.002 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.377 Fit side-chains REVERT: A 78 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7779 (mp) REVERT: A 268 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7700 (mttp) outliers start: 11 outliers final: 6 residues processed: 52 average time/residue: 1.1661 time to fit residues: 62.8332 Evaluate side-chains 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.0370 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 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 = 0.132179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115337 restraints weight = 3325.395| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.26 r_work: 0.3215 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3566 Z= 0.190 Angle : 0.604 12.820 4874 Z= 0.262 Chirality : 0.040 0.136 509 Planarity : 0.003 0.027 579 Dihedral : 11.641 89.356 560 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.59 % Allowed : 19.31 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.41), residues: 397 helix: 2.13 (0.35), residues: 204 sheet: 0.22 (0.56), residues: 82 loop : -0.26 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 25 HIS 0.004 0.001 HIS A 69 PHE 0.008 0.001 PHE A 218 TYR 0.013 0.001 TYR A 144 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.364 Fit side-chains REVERT: A 78 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7753 (mp) REVERT: A 268 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7661 (mttp) outliers start: 9 outliers final: 4 residues processed: 54 average time/residue: 1.2011 time to fit residues: 67.1134 Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115146 restraints weight = 3343.549| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.27 r_work: 0.3212 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3566 Z= 0.196 Angle : 0.609 12.881 4874 Z= 0.264 Chirality : 0.041 0.135 509 Planarity : 0.003 0.026 579 Dihedral : 11.725 88.661 560 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.02 % Allowed : 20.46 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.41), residues: 397 helix: 2.17 (0.35), residues: 204 sheet: 0.20 (0.56), residues: 82 loop : -0.30 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 25 HIS 0.004 0.001 HIS A 69 PHE 0.007 0.001 PHE A 218 TYR 0.014 0.001 TYR A 144 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.425 Fit side-chains REVERT: A 78 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7766 (mp) REVERT: A 268 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7681 (mttp) outliers start: 7 outliers final: 4 residues processed: 53 average time/residue: 1.1348 time to fit residues: 62.3614 Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114471 restraints weight = 3352.176| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.27 r_work: 0.3203 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3566 Z= 0.216 Angle : 0.624 12.834 4874 Z= 0.274 Chirality : 0.041 0.135 509 Planarity : 0.003 0.027 579 Dihedral : 11.838 86.775 560 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.02 % Allowed : 20.75 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.41), residues: 397 helix: 2.13 (0.34), residues: 204 sheet: 0.19 (0.56), residues: 82 loop : -0.31 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 25 HIS 0.005 0.001 HIS A 69 PHE 0.008 0.001 PHE A 224 TYR 0.015 0.002 TYR A 144 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.326 Fit side-chains REVERT: A 78 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7773 (mp) REVERT: A 268 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7682 (mttp) outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 1.1966 time to fit residues: 63.1350 Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.130398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113459 restraints weight = 3273.811| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.25 r_work: 0.3192 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3566 Z= 0.246 Angle : 0.646 12.716 4874 Z= 0.286 Chirality : 0.042 0.136 509 Planarity : 0.003 0.028 579 Dihedral : 12.113 86.511 560 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.59 % Allowed : 19.88 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.41), residues: 397 helix: 2.03 (0.34), residues: 204 sheet: 0.17 (0.56), residues: 82 loop : -0.34 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 25 HIS 0.005 0.001 HIS A 69 PHE 0.009 0.001 PHE A 224 TYR 0.016 0.002 TYR A 144 ARG 0.002 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.390 Fit side-chains REVERT: A 78 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7756 (mp) REVERT: A 241 HIS cc_start: 0.7504 (p-80) cc_final: 0.7245 (p90) REVERT: A 268 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7689 (mttp) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 1.1635 time to fit residues: 62.6329 Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 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 = 0.130146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.113084 restraints weight = 3331.258| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.27 r_work: 0.3185 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3566 Z= 0.261 Angle : 0.656 12.520 4874 Z= 0.292 Chirality : 0.043 0.137 509 Planarity : 0.003 0.029 579 Dihedral : 12.217 87.206 560 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.88 % Allowed : 19.60 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.41), residues: 397 helix: 2.01 (0.34), residues: 204 sheet: 0.18 (0.55), residues: 82 loop : -0.40 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 25 HIS 0.006 0.001 HIS A 69 PHE 0.009 0.001 PHE A 224 TYR 0.016 0.002 TYR A 144 ARG 0.002 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.374 Fit side-chains REVERT: A 78 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7767 (mp) REVERT: A 241 HIS cc_start: 0.7620 (p-80) cc_final: 0.7384 (p90) REVERT: A 268 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7698 (mttp) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 1.1484 time to fit residues: 61.7879 Evaluate side-chains 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 349 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.130679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113727 restraints weight = 3292.057| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.26 r_work: 0.3194 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3566 Z= 0.233 Angle : 0.640 12.652 4874 Z= 0.283 Chirality : 0.042 0.137 509 Planarity : 0.003 0.028 579 Dihedral : 12.107 88.009 560 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.31 % Allowed : 20.75 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.41), residues: 397 helix: 2.04 (0.34), residues: 204 sheet: 0.17 (0.56), residues: 82 loop : -0.42 (0.57), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 25 HIS 0.005 0.001 HIS A 69 PHE 0.009 0.001 PHE A 224 TYR 0.015 0.002 TYR A 144 ARG 0.001 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.411 Fit side-chains REVERT: A 78 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7799 (mp) REVERT: A 241 HIS cc_start: 0.7619 (p-80) cc_final: 0.7367 (p90) REVERT: A 268 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7685 (mttp) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 1.1901 time to fit residues: 61.5851 Evaluate side-chains 54 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 349 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 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 = 0.132793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115907 restraints weight = 3324.465| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.27 r_work: 0.3221 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3566 Z= 0.185 Angle : 0.596 12.556 4874 Z= 0.259 Chirality : 0.040 0.134 509 Planarity : 0.003 0.028 579 Dihedral : 11.687 89.610 560 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.02 % Allowed : 21.04 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.42), residues: 397 helix: 2.20 (0.35), residues: 204 sheet: 0.19 (0.56), residues: 82 loop : -0.40 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 25 HIS 0.004 0.001 HIS A 69 PHE 0.008 0.001 PHE A 218 TYR 0.013 0.001 TYR A 144 ARG 0.001 0.000 ARG A 195 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.386 Fit side-chains REVERT: A 78 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7749 (mp) REVERT: A 241 HIS cc_start: 0.7596 (p-80) cc_final: 0.7347 (p90) REVERT: A 268 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7654 (mttp) outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 1.1489 time to fit residues: 64.2073 Evaluate side-chains 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 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 = 0.130932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113955 restraints weight = 3341.819| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.27 r_work: 0.3199 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3566 Z= 0.229 Angle : 0.637 12.674 4874 Z= 0.281 Chirality : 0.042 0.135 509 Planarity : 0.003 0.029 579 Dihedral : 12.029 89.443 560 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.02 % Allowed : 22.48 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.41), residues: 397 helix: 2.10 (0.34), residues: 204 sheet: 0.16 (0.56), residues: 82 loop : -0.40 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 25 HIS 0.005 0.001 HIS A 69 PHE 0.008 0.001 PHE A 224 TYR 0.016 0.002 TYR A 144 ARG 0.001 0.000 ARG A 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2928.03 seconds wall clock time: 52 minutes 19.21 seconds (3139.21 seconds total)