Starting phenix.real_space_refine on Wed Mar 5 20:49:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qt9_18646/03_2025/8qt9_18646.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qt9_18646/03_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_18646/03_2025/8qt9_18646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qt9_18646/03_2025/8qt9_18646.map" model { file = "/net/cci-nas-00/data/ceres_data/8qt9_18646/03_2025/8qt9_18646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qt9_18646/03_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-5624/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: 3.92, per 1000 atoms: 1.12 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: 1.03 Conformation dependent library (CDL) restraints added in 390.8 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: 0.37 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: 1.03 Time building geometry restraints manager: 1.21 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: 2.260 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.020 Find NCS groups from input model: 0.030 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:14.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.860 ------------------------------------------------------------------------------- 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 : 0.398 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 1.2002 time to fit residues: 58.3854 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 : 0.369 ------------------------------------------------------------------------------- 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: 0.5980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.131377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114578 restraints weight = 3274.686| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.25 r_work: 0.3204 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.0770 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= 0.213 Angle : 0.648 13.706 4874 Z= 0.279 Chirality : 0.042 0.140 509 Planarity : 0.003 0.027 579 Dihedral : 12.380 85.668 564 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.09 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: 1.58 (0.42), residues: 397 helix: 2.02 (0.35), residues: 204 sheet: 0.25 (0.56), residues: 82 loop : -0.03 (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 0.007 0.001 PHE A 32 TYR 0.015 0.001 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 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.402 Fit side-chains REVERT: A 78 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7779 (mp) outliers start: 9 outliers final: 4 residues processed: 54 average time/residue: 1.1160 time to fit residues: 62.6767 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 : 0.394 ------------------------------------------------------------------------------- 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: 0.9980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.131370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114553 restraints weight = 3287.574| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.25 r_work: 0.3203 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3566 Z= 0.210 Angle : 0.624 12.874 4874 Z= 0.271 Chirality : 0.041 0.137 509 Planarity : 0.003 0.027 579 Dihedral : 11.657 86.729 560 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.59 % Allowed : 19.60 % Favored : 77.81 % 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: 1.62 (0.42), residues: 397 helix: 2.11 (0.35), residues: 204 sheet: 0.23 (0.56), residues: 82 loop : -0.13 (0.60), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 25 HIS 0.004 0.001 HIS A 69 PHE 0.008 0.001 PHE A 218 TYR 0.014 0.002 TYR A 144 ARG 0.002 0.000 ARG A 195 *********************** 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 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.394 Fit side-chains REVERT: A 78 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 268 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7683 (mttp) outliers start: 9 outliers final: 4 residues processed: 52 average time/residue: 1.2466 time to fit residues: 67.1547 Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 268 LYS Chi-restraints excluded: chain A residue 312 GLN 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: 1.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.130712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113786 restraints weight = 3328.318| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.26 r_work: 0.3194 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.0939 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= 0.231 Angle : 0.638 12.803 4874 Z= 0.280 Chirality : 0.042 0.136 509 Planarity : 0.003 0.028 579 Dihedral : 11.860 86.004 560 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 : 3.17 % Allowed : 18.44 % 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: 1.52 (0.42), residues: 397 helix: 2.06 (0.35), residues: 204 sheet: 0.18 (0.56), residues: 82 loop : -0.24 (0.59), 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 0.001 0.000 ARG A 51 *********************** 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: 11 poor density : 47 time to evaluate : 0.395 Fit side-chains REVERT: A 78 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7753 (mp) REVERT: A 268 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7686 (mttp) outliers start: 11 outliers final: 7 residues processed: 52 average time/residue: 1.0996 time to fit residues: 59.2803 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 : 0.382 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 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 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 = 0.3506 r_free = 0.3506 target = 0.131754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114854 restraints weight = 3352.807| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.27 r_work: 0.3209 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3566 Z= 0.203 Angle : 0.613 12.819 4874 Z= 0.267 Chirality : 0.041 0.135 509 Planarity : 0.003 0.027 579 Dihedral : 11.683 88.021 560 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.23 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: 1.59 (0.42), residues: 397 helix: 2.15 (0.35), residues: 204 sheet: 0.19 (0.56), residues: 82 loop : -0.26 (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 0.002 TYR A 144 ARG 0.001 0.000 ARG A 195 *********************** 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 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.334 Fit side-chains REVERT: A 78 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7768 (mp) REVERT: A 268 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7678 (mttp) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 1.0572 time to fit residues: 55.9031 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 : 0.348 ------------------------------------------------------------------------------- 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 392 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.131981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115047 restraints weight = 3353.079| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.28 r_work: 0.3211 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3566 Z= 0.199 Angle : 0.609 12.831 4874 Z= 0.264 Chirality : 0.041 0.134 509 Planarity : 0.003 0.026 579 Dihedral : 11.695 88.280 560 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.31 % Allowed : 20.17 % 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: 1.62 (0.42), residues: 397 helix: 2.20 (0.35), residues: 204 sheet: 0.20 (0.56), residues: 82 loop : -0.29 (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 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 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.387 Fit side-chains REVERT: A 78 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7768 (mp) REVERT: A 268 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7678 (mttp) outliers start: 8 outliers final: 6 residues processed: 53 average time/residue: 1.1778 time to fit residues: 64.6562 Evaluate side-chains 56 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 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 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: 0.8980 chunk 33 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 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 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 = 0.3509 r_free = 0.3509 target = 0.131992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115127 restraints weight = 3288.115| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.26 r_work: 0.3213 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3566 Z= 0.202 Angle : 0.612 12.793 4874 Z= 0.267 Chirality : 0.041 0.134 509 Planarity : 0.003 0.027 579 Dihedral : 11.726 88.086 560 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.17 % Allowed : 19.88 % 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: 1.59 (0.42), residues: 397 helix: 2.17 (0.35), residues: 204 sheet: 0.21 (0.56), residues: 82 loop : -0.33 (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 224 TYR 0.014 0.002 TYR A 144 ARG 0.001 0.000 ARG A 195 *********************** 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 58 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.376 Fit side-chains REVERT: A 78 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7767 (mp) REVERT: A 268 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7680 (mttp) outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 1.1337 time to fit residues: 59.9643 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 : 0.391 ------------------------------------------------------------------------------- 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: 1.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 37 optimal weight: 0.0970 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.131818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114842 restraints weight = 3342.731| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.27 r_work: 0.3207 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3566 Z= 0.205 Angle : 0.613 12.779 4874 Z= 0.268 Chirality : 0.041 0.133 509 Planarity : 0.003 0.027 579 Dihedral : 11.749 87.789 560 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.09 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: 1.59 (0.42), residues: 397 helix: 2.18 (0.35), residues: 204 sheet: 0.20 (0.56), residues: 82 loop : -0.32 (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 0.008 0.001 PHE A 224 TYR 0.014 0.002 TYR A 144 ARG 0.001 0.000 ARG A 195 *********************** 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: 9 poor density : 48 time to evaluate : 0.369 Fit side-chains REVERT: A 78 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7775 (mp) REVERT: A 241 HIS cc_start: 0.7532 (p-80) cc_final: 0.7300 (p90) REVERT: A 268 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7685 (mttp) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 1.0960 time to fit residues: 59.0708 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 : 0.340 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.131520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114576 restraints weight = 3299.082| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.26 r_work: 0.3205 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3566 Z= 0.215 Angle : 0.621 12.771 4874 Z= 0.272 Chirality : 0.041 0.134 509 Planarity : 0.003 0.027 579 Dihedral : 11.818 86.879 560 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.88 % Allowed : 19.88 % 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: 2.14 (0.35), residues: 204 sheet: 0.19 (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 0.008 0.001 PHE A 224 TYR 0.015 0.002 TYR A 144 ARG 0.001 0.000 ARG A 195 *********************** 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 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.371 Fit side-chains REVERT: A 78 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7783 (mp) REVERT: A 241 HIS cc_start: 0.7563 (p-80) cc_final: 0.7322 (p90) REVERT: A 268 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7690 (mttp) outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 1.1206 time to fit residues: 60.3858 Evaluate side-chains 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.0270 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.0000 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.5042 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.132424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115568 restraints weight = 3341.825| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.27 r_work: 0.3222 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3566 Z= 0.185 Angle : 0.593 12.565 4874 Z= 0.257 Chirality : 0.040 0.133 509 Planarity : 0.003 0.028 579 Dihedral : 11.640 89.822 560 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: 1.65 (0.42), residues: 397 helix: 2.24 (0.35), residues: 204 sheet: 0.21 (0.56), residues: 82 loop : -0.32 (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 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 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.394 Fit side-chains REVERT: A 78 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7703 (mp) REVERT: A 241 HIS cc_start: 0.7574 (p-80) cc_final: 0.7340 (p90) REVERT: A 268 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7644 (mttp) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 1.0995 time to fit residues: 58.1135 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 : 0.385 ------------------------------------------------------------------------------- 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 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 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 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 = 0.3499 r_free = 0.3499 target = 0.131089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.114005 restraints weight = 3353.163| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.28 r_work: 0.3196 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1002 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 : 0.634 12.762 4874 Z= 0.279 Chirality : 0.042 0.134 509 Planarity : 0.003 0.028 579 Dihedral : 11.995 88.367 560 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.31 % Allowed : 21.04 % Favored : 76.66 % 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: 1.51 (0.41), residues: 397 helix: 2.11 (0.34), residues: 204 sheet: 0.17 (0.56), residues: 82 loop : -0.35 (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 195 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2987.81 seconds wall clock time: 51 minutes 37.80 seconds (3097.80 seconds total)