Starting phenix.real_space_refine on Sat Apr 26 22:12:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qt9_18646/04_2025/8qt9_18646.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qt9_18646/04_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_18646/04_2025/8qt9_18646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qt9_18646/04_2025/8qt9_18646.map" model { file = "/net/cci-nas-00/data/ceres_data/8qt9_18646/04_2025/8qt9_18646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qt9_18646/04_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-5669/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: 3.29, per 1000 atoms: 0.94 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: 1.15 Conformation dependent library (CDL) restraints added in 435.6 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: 0.38 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: 1.12 Time building geometry restraints manager: 1.23 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: 1.830 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: 0.030 Set scattering table: 0.030 Process input model: 14.820 Find NCS groups from input model: 0.040 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:15.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.580 ------------------------------------------------------------------------------- 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 3568 Z= 0.250 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 Details of bonding type rmsd hydrogen bonds : bond 0.13953 ( 193) hydrogen bonds : angle 7.13357 ( 555) covalent geometry : bond 0.00521 ( 3566) covalent geometry : angle 0.68489 ( 4874) Misc. bond : bond 0.05061 ( 2) *********************** 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 : 0.381 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 1.3849 time to fit residues: 67.2745 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 : 0.395 ------------------------------------------------------------------------------- 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 : 0.005 0.158 3568 Z= 0.139 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 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 193) hydrogen bonds : angle 4.80349 ( 555) covalent geometry : bond 0.00315 ( 3566) covalent geometry : angle 0.64833 ( 4874) Misc. bond : bond 0.15055 ( 2) *********************** 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 : 0.359 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: 1.0013 time to fit residues: 56.2797 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 : 0.380 ------------------------------------------------------------------------------- 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: 0.9980 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 : 0.005 0.147 3568 Z= 0.136 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 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 193) hydrogen bonds : angle 4.66739 ( 555) covalent geometry : bond 0.00311 ( 3566) covalent geometry : angle 0.62411 ( 4874) Misc. bond : bond 0.14305 ( 2) *********************** 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 : 0.531 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: 1.1793 time to fit residues: 63.6738 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 : 0.346 ------------------------------------------------------------------------------- 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: 0.5980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3498 r_free = 0.3498 target = 0.131061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.114136 restraints weight = 3331.080| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.27 r_work: 0.3198 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.145 3568 Z= 0.142 Angle : 0.630 12.849 4874 Z= 0.275 Chirality : 0.041 0.136 509 Planarity : 0.003 0.027 579 Dihedral : 11.777 86.253 560 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: 2.09 (0.35), residues: 204 sheet: 0.19 (0.56), residues: 82 loop : -0.23 (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 0.015 0.002 TYR A 144 ARG 0.001 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 193) hydrogen bonds : angle 4.67032 ( 555) covalent geometry : bond 0.00326 ( 3566) covalent geometry : angle 0.62969 ( 4874) Misc. bond : bond 0.14023 ( 2) *********************** 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 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 Fit side-chains REVERT: A 78 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7784 (mp) REVERT: A 268 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7685 (mttp) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 1.1632 time to fit residues: 61.4364 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=3.50 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 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 A 241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114279 restraints weight = 3363.270| |-----------------------------------------------------------------------------| 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: 2.82 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 3568 Z= 0.132 Angle : 0.617 12.857 4874 Z= 0.269 Chirality : 0.041 0.135 509 Planarity : 0.003 0.027 579 Dihedral : 11.702 87.576 560 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.88 % Allowed : 19.31 % 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: 1.58 (0.41), residues: 397 helix: 2.13 (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 Details of bonding type rmsd hydrogen bonds : bond 0.03969 ( 193) hydrogen bonds : angle 4.63066 ( 555) covalent geometry : bond 0.00304 ( 3566) covalent geometry : angle 0.61655 ( 4874) Misc. bond : bond 0.13847 ( 2) *********************** 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 57 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.331 Fit side-chains REVERT: A 78 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7775 (mp) REVERT: A 268 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7680 (mttp) outliers start: 10 outliers final: 7 residues processed: 52 average time/residue: 1.1310 time to fit residues: 60.9854 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 : 0.373 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.132313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115422 restraints weight = 3354.268| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.27 r_work: 0.3215 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 3568 Z= 0.123 Angle : 0.600 12.701 4874 Z= 0.260 Chirality : 0.040 0.134 509 Planarity : 0.003 0.027 579 Dihedral : 11.638 89.148 560 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.09 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: 1.64 (0.42), residues: 397 helix: 2.22 (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 195 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 193) hydrogen bonds : angle 4.56214 ( 555) covalent geometry : bond 0.00283 ( 3566) covalent geometry : angle 0.60050 ( 4874) Misc. bond : bond 0.13365 ( 2) *********************** 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 59 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.404 Fit side-chains REVERT: A 78 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7738 (mp) REVERT: A 268 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7672 (mttp) outliers start: 10 outliers final: 6 residues processed: 54 average time/residue: 1.1455 time to fit residues: 64.1535 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 : 0.359 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.0000 chunk 14 optimal weight: 0.4980 chunk 33 optimal weight: 0.0050 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.0970 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.136046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119466 restraints weight = 3292.602| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.26 r_work: 0.3266 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 3568 Z= 0.095 Angle : 0.544 11.166 4874 Z= 0.237 Chirality : 0.039 0.132 509 Planarity : 0.003 0.025 579 Dihedral : 11.147 84.703 560 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.02 % Allowed : 21.90 % Favored : 76.08 % 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: 1.84 (0.42), residues: 397 helix: 2.43 (0.35), residues: 204 sheet: 0.25 (0.57), residues: 82 loop : -0.28 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 25 HIS 0.003 0.001 HIS A 69 PHE 0.007 0.001 PHE A 218 TYR 0.011 0.001 TYR A 275 ARG 0.001 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 193) hydrogen bonds : angle 4.36933 ( 555) covalent geometry : bond 0.00225 ( 3566) covalent geometry : angle 0.54409 ( 4874) Misc. bond : bond 0.11479 ( 2) *********************** 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: 7 poor density : 51 time to evaluate : 0.403 Fit side-chains REVERT: A 78 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7683 (mp) REVERT: A 264 GLN cc_start: 0.8068 (mt0) cc_final: 0.7665 (mm-40) REVERT: A 268 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7584 (mttp) REVERT: A 381 LYS cc_start: 0.7052 (mtmt) cc_final: 0.5763 (tmmt) outliers start: 7 outliers final: 2 residues processed: 55 average time/residue: 1.1596 time to fit residues: 66.0268 Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 191 THR Chi-restraints excluded: chain A residue 268 LYS 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: 1.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 0.0370 chunk 37 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.132592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115591 restraints weight = 3349.754| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.27 r_work: 0.3217 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 3568 Z= 0.126 Angle : 0.601 12.649 4874 Z= 0.262 Chirality : 0.041 0.133 509 Planarity : 0.003 0.025 579 Dihedral : 11.669 88.330 560 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.73 % Allowed : 23.05 % Favored : 75.22 % 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: 1.71 (0.42), residues: 397 helix: 2.31 (0.35), residues: 204 sheet: 0.17 (0.56), residues: 82 loop : -0.28 (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 0.002 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 193) hydrogen bonds : angle 4.50102 ( 555) covalent geometry : bond 0.00292 ( 3566) covalent geometry : angle 0.60094 ( 4874) Misc. bond : bond 0.12146 ( 2) *********************** 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 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.371 Fit side-chains REVERT: A 78 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7768 (mp) REVERT: A 268 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7674 (mttp) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 1.2126 time to fit residues: 63.9431 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 : 0.390 ------------------------------------------------------------------------------- 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 191 THR Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 312 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 312 GLN 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 = 0.131347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114273 restraints weight = 3300.410| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.26 r_work: 0.3201 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.005 0.140 3568 Z= 0.145 Angle : 0.631 12.882 4874 Z= 0.277 Chirality : 0.042 0.133 509 Planarity : 0.003 0.028 579 Dihedral : 11.931 88.085 560 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.02 % Allowed : 21.90 % Favored : 76.08 % 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 (0.42), residues: 397 helix: 2.20 (0.35), residues: 204 sheet: 0.19 (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 0.005 0.001 HIS A 69 PHE 0.008 0.001 PHE A 224 TYR 0.016 0.002 TYR A 144 ARG 0.002 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 193) hydrogen bonds : angle 4.61938 ( 555) covalent geometry : bond 0.00334 ( 3566) covalent geometry : angle 0.63114 ( 4874) Misc. bond : bond 0.13207 ( 2) *********************** 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 55 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.393 Fit side-chains REVERT: A 78 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7752 (mp) REVERT: A 241 HIS cc_start: 0.7534 (p-80) cc_final: 0.7292 (p90) REVERT: A 268 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7682 (mttp) outliers start: 7 outliers final: 3 residues processed: 53 average time/residue: 1.1501 time to fit residues: 63.1187 Evaluate side-chains 53 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 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 191 THR Chi-restraints excluded: chain A residue 268 LYS 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: 0.6980 chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.132433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115528 restraints weight = 3342.913| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.26 r_work: 0.3223 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 3568 Z= 0.119 Angle : 0.594 12.599 4874 Z= 0.258 Chirality : 0.040 0.132 509 Planarity : 0.003 0.027 579 Dihedral : 11.649 89.783 560 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.15 % Allowed : 22.77 % Favored : 76.08 % 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: 1.67 (0.42), residues: 397 helix: 2.28 (0.35), residues: 204 sheet: 0.16 (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 0.002 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 193) hydrogen bonds : angle 4.49545 ( 555) covalent geometry : bond 0.00276 ( 3566) covalent geometry : angle 0.59370 ( 4874) Misc. bond : bond 0.12355 ( 2) ********************** 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 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.407 Fit side-chains REVERT: A 78 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7726 (mp) REVERT: A 241 HIS cc_start: 0.7592 (p-80) cc_final: 0.7362 (p90) REVERT: A 268 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7659 (mttp) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 1.1272 time to fit residues: 59.5652 Evaluate side-chains 51 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 191 THR Chi-restraints excluded: chain A residue 268 LYS 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: 0.4980 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 312 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.131179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.114061 restraints weight = 3361.709| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.28 r_work: 0.3198 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 3568 Z= 0.149 Angle : 0.636 12.972 4874 Z= 0.280 Chirality : 0.042 0.133 509 Planarity : 0.003 0.027 579 Dihedral : 11.995 88.869 560 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.73 % Allowed : 22.48 % Favored : 75.79 % 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 (0.41), residues: 397 helix: 2.16 (0.35), residues: 204 sheet: 0.16 (0.56), residues: 82 loop : -0.36 (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 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 193) hydrogen bonds : angle 4.62541 ( 555) covalent geometry : bond 0.00345 ( 3566) covalent geometry : angle 0.63650 ( 4874) Misc. bond : bond 0.13058 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3052.66 seconds wall clock time: 52 minutes 54.04 seconds (3174.04 seconds total)