Starting phenix.real_space_refine on Wed Jun 4 17:51:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tx6_26155/06_2025/7tx6_26155.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tx6_26155/06_2025/7tx6_26155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tx6_26155/06_2025/7tx6_26155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tx6_26155/06_2025/7tx6_26155.map" model { file = "/net/cci-nas-00/data/ceres_data/7tx6_26155/06_2025/7tx6_26155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tx6_26155/06_2025/7tx6_26155.cif" } resolution = 3.3 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= 0.002 sd= 0.033 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: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 2122 2.51 5 N 503 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3169 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3094 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 13, 'TRANS': 384} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 10, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'AJP': 1, 'MTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'MTX:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.10, per 1000 atoms: 0.98 Number of scatterers: 3169 At special positions: 0 Unit cell: (72.36, 61.56, 79.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 534 8.00 N 503 7.00 C 2122 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 403.4 milliseconds 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB MTX A2644 " Number of C-beta restraints generated: 752 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 88.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 removed outlier: 4.105A pdb=" N HIS A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 67 through 90 removed outlier: 3.835A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.986A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 113 removed outlier: 3.861A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.562A pdb=" N ALA A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.906A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 177 removed outlier: 3.538A pdb=" N VAL A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 removed outlier: 3.616A pdb=" N PHE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.936A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 296 removed outlier: 3.511A pdb=" N ARG A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 326 removed outlier: 4.015A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 328 No H-bonds generated for 'chain 'A' and resid 327 through 328' Processing helix chain 'A' and resid 329 through 334 removed outlier: 4.097A pdb=" N ARG A 333 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP A 334 " --> pdb=" O TRP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 389 removed outlier: 3.702A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 392 through 419 removed outlier: 3.726A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 459 removed outlier: 3.664A pdb=" N GLN A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) 239 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.97 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: 1.18 - 1.31: 446 1.31 - 1.43: 993 1.43 - 1.56: 1806 1.56 - 1.68: 5 1.68 - 1.81: 15 Bond restraints: 3265 Sorted by residual: bond pdb=" C VAL A 410 " pdb=" N LYS A 411 " ideal model delta sigma weight residual 1.335 1.449 -0.114 1.31e-02 5.83e+03 7.53e+01 bond pdb=" C4 MTX A2644 " pdb=" NA4 MTX A2644 " ideal model delta sigma weight residual 1.328 1.449 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" N MTX A2644 " pdb=" C MTX A2644 " ideal model delta sigma weight residual 1.339 1.455 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C2 MTX A2644 " pdb=" NA2 MTX A2644 " ideal model delta sigma weight residual 1.341 1.451 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C14 MTX A2644 " pdb=" N10 MTX A2644 " ideal model delta sigma weight residual 1.368 1.453 -0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 3260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 4147 1.56 - 3.11: 237 3.11 - 4.67: 79 4.67 - 6.23: 13 6.23 - 7.79: 4 Bond angle restraints: 4480 Sorted by residual: angle pdb=" C VAL A 410 " pdb=" N LYS A 411 " pdb=" CA LYS A 411 " ideal model delta sigma weight residual 120.28 114.07 6.21 1.34e+00 5.57e-01 2.15e+01 angle pdb=" CA ILE A 48 " pdb=" C ILE A 48 " pdb=" O ILE A 48 " ideal model delta sigma weight residual 121.17 116.45 4.72 1.06e+00 8.90e-01 1.98e+01 angle pdb=" CA ILE A 417 " pdb=" C ILE A 417 " pdb=" O ILE A 417 " ideal model delta sigma weight residual 120.85 116.34 4.51 1.06e+00 8.90e-01 1.81e+01 angle pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 120.57 116.30 4.27 1.07e+00 8.73e-01 1.59e+01 angle pdb=" N PHE A 416 " pdb=" CA PHE A 416 " pdb=" C PHE A 416 " ideal model delta sigma weight residual 111.28 106.94 4.34 1.09e+00 8.42e-01 1.58e+01 ... (remaining 4475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 1837 24.23 - 48.46: 81 48.46 - 72.69: 7 72.69 - 96.92: 8 96.92 - 121.14: 7 Dihedral angle restraints: 1940 sinusoidal: 769 harmonic: 1171 Sorted by residual: dihedral pdb=" C02 AJP A2501 " pdb=" C85 AJP A2501 " pdb=" O84 AJP A2501 " pdb=" C05 AJP A2501 " ideal model delta sinusoidal sigma weight residual -57.60 63.54 -121.14 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" C28 AJP A2501 " pdb=" C26 AJP A2501 " pdb=" C27 AJP A2501 " pdb=" O31 AJP A2501 " ideal model delta sinusoidal sigma weight residual -54.31 65.16 -119.47 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" O31 AJP A2501 " pdb=" C26 AJP A2501 " pdb=" C27 AJP A2501 " pdb=" O78 AJP A2501 " ideal model delta sinusoidal sigma weight residual 175.34 56.37 118.97 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 1937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 469 0.070 - 0.141: 50 0.141 - 0.211: 12 0.211 - 0.281: 6 0.281 - 0.352: 1 Chirality restraints: 538 Sorted by residual: chirality pdb=" C11 AJP A2501 " pdb=" C10 AJP A2501 " pdb=" C12 AJP A2501 " pdb=" C16 AJP A2501 " both_signs ideal model delta sigma weight residual False 2.20 2.56 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C15 AJP A2501 " pdb=" C14 AJP A2501 " pdb=" C16 AJP A2501 " pdb=" C20 AJP A2501 " both_signs ideal model delta sigma weight residual False -2.42 -2.70 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C23 AJP A2501 " pdb=" C22 AJP A2501 " pdb=" C24 AJP A2501 " pdb=" O25 AJP A2501 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 535 not shown) Planarity restraints: 529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 62 " -0.016 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C GLU A 62 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU A 62 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN A 63 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 93 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO A 94 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 68 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C ILE A 68 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE A 68 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 69 " 0.011 2.00e-02 2.50e+03 ... (remaining 526 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1092 2.84 - 3.36: 3421 3.36 - 3.87: 5070 3.87 - 4.39: 5536 4.39 - 4.90: 9405 Nonbonded interactions: 24524 Sorted by model distance: nonbonded pdb=" OD1 ASN A 300 " pdb=" N SER A 301 " model vdw 2.327 3.120 nonbonded pdb=" OD1 ASP A 56 " pdb=" N LYS A 57 " model vdw 2.386 3.120 nonbonded pdb=" O SER A 102 " pdb=" OG SER A 105 " model vdw 2.421 3.040 nonbonded pdb=" O LEU A 440 " pdb=" OG SER A 443 " model vdw 2.482 3.040 nonbonded pdb=" O THR A 87 " pdb=" O LEU A 90 " model vdw 2.484 3.040 ... (remaining 24519 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: 0.620 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.180 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.121 3266 Z= 0.476 Angle : 0.902 7.786 4480 Z= 0.564 Chirality : 0.055 0.352 538 Planarity : 0.005 0.071 529 Dihedral : 17.014 121.145 1188 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.62 % Allowed : 6.88 % Favored : 92.50 % Cbeta Deviations : 0.27 % 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: 2.51 (0.42), residues: 394 helix: 2.27 (0.28), residues: 313 sheet: None (None), residues: 0 loop : -0.83 (0.73), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.002 0.001 HIS A 355 PHE 0.010 0.001 PHE A 405 TYR 0.013 0.001 TYR A 438 ARG 0.002 0.000 ARG A 133 Details of bonding type rmsd hydrogen bonds : bond 0.16694 ( 239) hydrogen bonds : angle 5.10258 ( 714) covalent geometry : bond 0.00798 ( 3265) covalent geometry : angle 0.90230 ( 4480) Misc. bond : bond 0.01909 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 103 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 282 TYR cc_start: 0.8319 (m-80) cc_final: 0.8030 (m-10) REVERT: A 287 TYR cc_start: 0.8372 (m-80) cc_final: 0.7722 (m-80) REVERT: A 363 TRP cc_start: 0.2795 (m100) cc_final: 0.2102 (m100) REVERT: A 395 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7789 (tt) outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.1498 time to fit residues: 18.7391 Evaluate side-chains 94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.130857 restraints weight = 5157.937| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.46 r_work: 0.3485 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3266 Z= 0.140 Angle : 0.662 8.553 4480 Z= 0.315 Chirality : 0.039 0.176 538 Planarity : 0.004 0.064 529 Dihedral : 9.241 73.889 571 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.56 % Allowed : 15.94 % Favored : 82.50 % Cbeta Deviations : 0.27 % 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: 3.22 (0.43), residues: 394 helix: 2.67 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -0.51 (0.81), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 334 HIS 0.002 0.001 HIS A 114 PHE 0.012 0.001 PHE A 432 TYR 0.013 0.001 TYR A 305 ARG 0.002 0.000 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.04932 ( 239) hydrogen bonds : angle 3.63769 ( 714) covalent geometry : bond 0.00293 ( 3265) covalent geometry : angle 0.66156 ( 4480) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.333 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 94 average time/residue: 0.1320 time to fit residues: 15.3831 Evaluate side-chains 90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 375 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.141737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.130306 restraints weight = 5064.749| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.36 r_work: 0.3489 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3266 Z= 0.134 Angle : 0.590 7.184 4480 Z= 0.290 Chirality : 0.037 0.119 538 Planarity : 0.004 0.060 529 Dihedral : 7.545 85.171 569 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.56 % Allowed : 21.56 % Favored : 76.88 % Cbeta Deviations : 0.27 % 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: 3.11 (0.43), residues: 394 helix: 2.70 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -1.01 (0.77), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 334 HIS 0.002 0.001 HIS A 358 PHE 0.010 0.001 PHE A 34 TYR 0.014 0.001 TYR A 305 ARG 0.004 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 239) hydrogen bonds : angle 3.43613 ( 714) covalent geometry : bond 0.00282 ( 3265) covalent geometry : angle 0.59037 ( 4480) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 133 ARG cc_start: 0.8506 (ttp-170) cc_final: 0.7980 (ptt180) outliers start: 5 outliers final: 4 residues processed: 91 average time/residue: 0.1376 time to fit residues: 15.3547 Evaluate side-chains 88 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 389 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.0670 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.142317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.130940 restraints weight = 5205.202| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.41 r_work: 0.3505 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3266 Z= 0.117 Angle : 0.570 9.430 4480 Z= 0.276 Chirality : 0.035 0.111 538 Planarity : 0.004 0.058 529 Dihedral : 7.304 87.877 569 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.94 % Allowed : 25.94 % Favored : 73.12 % Cbeta Deviations : 0.27 % 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: 3.23 (0.43), residues: 394 helix: 2.66 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -0.53 (0.83), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.002 0.001 HIS A 114 PHE 0.011 0.001 PHE A 165 TYR 0.010 0.001 TYR A 438 ARG 0.004 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 239) hydrogen bonds : angle 3.31800 ( 714) covalent geometry : bond 0.00244 ( 3265) covalent geometry : angle 0.57043 ( 4480) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 102 SER cc_start: 0.9086 (m) cc_final: 0.8753 (p) REVERT: A 119 MET cc_start: 0.8554 (mmm) cc_final: 0.8269 (mmm) outliers start: 3 outliers final: 2 residues processed: 87 average time/residue: 0.1366 time to fit residues: 14.5699 Evaluate side-chains 87 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 301 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.140838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.129486 restraints weight = 5173.354| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.44 r_work: 0.3482 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3266 Z= 0.128 Angle : 0.569 7.541 4480 Z= 0.277 Chirality : 0.035 0.112 538 Planarity : 0.004 0.056 529 Dihedral : 7.113 82.871 569 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.50 % Allowed : 24.69 % Favored : 72.81 % Cbeta Deviations : 0.27 % 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: 3.27 (0.43), residues: 394 helix: 2.73 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.63 (0.82), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 334 HIS 0.002 0.001 HIS A 358 PHE 0.010 0.001 PHE A 34 TYR 0.010 0.001 TYR A 438 ARG 0.002 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04390 ( 239) hydrogen bonds : angle 3.31765 ( 714) covalent geometry : bond 0.00270 ( 3265) covalent geometry : angle 0.56853 ( 4480) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 102 SER cc_start: 0.9077 (m) cc_final: 0.8583 (p) REVERT: A 133 ARG cc_start: 0.8509 (ttp-170) cc_final: 0.7965 (ptt180) outliers start: 8 outliers final: 5 residues processed: 91 average time/residue: 0.1461 time to fit residues: 16.4076 Evaluate side-chains 90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 389 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 0.0040 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 7 optimal weight: 0.0030 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.146029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.135129 restraints weight = 5245.980| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.36 r_work: 0.3543 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3266 Z= 0.102 Angle : 0.592 11.310 4480 Z= 0.269 Chirality : 0.034 0.111 538 Planarity : 0.004 0.056 529 Dihedral : 7.013 81.958 569 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.25 % Allowed : 27.19 % Favored : 71.56 % Cbeta Deviations : 0.27 % 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: 3.49 (0.43), residues: 394 helix: 2.89 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -0.77 (0.82), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.001 0.000 HIS A 355 PHE 0.010 0.001 PHE A 165 TYR 0.009 0.001 TYR A 376 ARG 0.004 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 239) hydrogen bonds : angle 3.15154 ( 714) covalent geometry : bond 0.00204 ( 3265) covalent geometry : angle 0.59165 ( 4480) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.303 Fit side-chains REVERT: A 102 SER cc_start: 0.9035 (m) cc_final: 0.8777 (p) REVERT: A 133 ARG cc_start: 0.8498 (ttp-170) cc_final: 0.8055 (ptt180) REVERT: A 195 PHE cc_start: 0.7226 (m-80) cc_final: 0.6835 (t80) REVERT: A 394 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8442 (tm-30) outliers start: 4 outliers final: 3 residues processed: 88 average time/residue: 0.1356 time to fit residues: 14.7626 Evaluate side-chains 87 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.140230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.128632 restraints weight = 5185.333| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.47 r_work: 0.3466 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3266 Z= 0.143 Angle : 0.612 10.430 4480 Z= 0.292 Chirality : 0.036 0.114 538 Planarity : 0.004 0.054 529 Dihedral : 7.112 82.320 569 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.56 % Allowed : 25.31 % Favored : 73.12 % Cbeta Deviations : 0.27 % 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: 3.38 (0.43), residues: 394 helix: 2.86 (0.28), residues: 317 sheet: None (None), residues: 0 loop : -0.59 (0.79), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 334 HIS 0.003 0.001 HIS A 358 PHE 0.010 0.001 PHE A 34 TYR 0.011 0.001 TYR A 35 ARG 0.003 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 239) hydrogen bonds : angle 3.32945 ( 714) covalent geometry : bond 0.00308 ( 3265) covalent geometry : angle 0.61168 ( 4480) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8055 (tt0) REVERT: A 102 SER cc_start: 0.9135 (m) cc_final: 0.8693 (p) REVERT: A 394 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8278 (tm-30) REVERT: A 395 LEU cc_start: 0.7410 (mt) cc_final: 0.7034 (mt) outliers start: 5 outliers final: 4 residues processed: 89 average time/residue: 0.1417 time to fit residues: 15.4878 Evaluate side-chains 87 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 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 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130456 restraints weight = 5158.456| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.39 r_work: 0.3503 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3266 Z= 0.123 Angle : 0.621 11.016 4480 Z= 0.289 Chirality : 0.035 0.111 538 Planarity : 0.004 0.054 529 Dihedral : 7.271 83.958 569 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.88 % Allowed : 25.62 % Favored : 72.50 % Cbeta Deviations : 0.27 % 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: 3.36 (0.43), residues: 394 helix: 2.79 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.66 (0.82), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 334 HIS 0.002 0.001 HIS A 358 PHE 0.009 0.001 PHE A 165 TYR 0.009 0.001 TYR A 438 ARG 0.005 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 239) hydrogen bonds : angle 3.25610 ( 714) covalent geometry : bond 0.00261 ( 3265) covalent geometry : angle 0.62110 ( 4480) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.352 Fit side-chains REVERT: A 99 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8163 (tt0) REVERT: A 102 SER cc_start: 0.9150 (m) cc_final: 0.8869 (p) REVERT: A 133 ARG cc_start: 0.8572 (ttp-170) cc_final: 0.8128 (ptt180) outliers start: 6 outliers final: 5 residues processed: 86 average time/residue: 0.1367 time to fit residues: 14.5599 Evaluate side-chains 86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.130288 restraints weight = 5241.850| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.46 r_work: 0.3495 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3266 Z= 0.126 Angle : 0.628 11.905 4480 Z= 0.293 Chirality : 0.035 0.112 538 Planarity : 0.004 0.054 529 Dihedral : 7.309 83.883 569 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.56 % Allowed : 25.62 % Favored : 72.81 % Cbeta Deviations : 0.27 % 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: 3.29 (0.43), residues: 394 helix: 2.72 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -0.72 (0.82), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.002 0.001 HIS A 358 PHE 0.012 0.001 PHE A 34 TYR 0.010 0.001 TYR A 35 ARG 0.005 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 239) hydrogen bonds : angle 3.28070 ( 714) covalent geometry : bond 0.00269 ( 3265) covalent geometry : angle 0.62810 ( 4480) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 102 SER cc_start: 0.9155 (m) cc_final: 0.8871 (p) REVERT: A 133 ARG cc_start: 0.8575 (ttp-170) cc_final: 0.8080 (ptt180) REVERT: A 195 PHE cc_start: 0.7246 (m-80) cc_final: 0.6986 (t80) outliers start: 5 outliers final: 5 residues processed: 85 average time/residue: 0.1477 time to fit residues: 15.3308 Evaluate side-chains 86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.141921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130568 restraints weight = 5158.757| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.48 r_work: 0.3513 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3266 Z= 0.126 Angle : 0.659 11.576 4480 Z= 0.301 Chirality : 0.035 0.111 538 Planarity : 0.004 0.054 529 Dihedral : 7.354 85.594 569 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.25 % Allowed : 26.25 % Favored : 72.50 % Cbeta Deviations : 0.27 % 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: 3.24 (0.43), residues: 394 helix: 2.71 (0.28), residues: 326 sheet: None (None), residues: 0 loop : -0.84 (0.79), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.002 0.001 HIS A 358 PHE 0.009 0.001 PHE A 165 TYR 0.010 0.001 TYR A 438 ARG 0.005 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 239) hydrogen bonds : angle 3.31936 ( 714) covalent geometry : bond 0.00269 ( 3265) covalent geometry : angle 0.65931 ( 4480) Misc. bond : bond 0.00018 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.327 Fit side-chains REVERT: A 102 SER cc_start: 0.9106 (m) cc_final: 0.8857 (p) outliers start: 4 outliers final: 4 residues processed: 84 average time/residue: 0.1412 time to fit residues: 14.7064 Evaluate side-chains 84 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.140246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128906 restraints weight = 5236.614| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.48 r_work: 0.3494 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3266 Z= 0.150 Angle : 0.666 11.830 4480 Z= 0.313 Chirality : 0.036 0.116 538 Planarity : 0.004 0.053 529 Dihedral : 7.496 87.609 569 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.56 % Allowed : 25.62 % Favored : 72.81 % Cbeta Deviations : 0.27 % 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: 3.14 (0.43), residues: 394 helix: 2.66 (0.28), residues: 323 sheet: None (None), residues: 0 loop : -0.83 (0.78), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 334 HIS 0.003 0.001 HIS A 358 PHE 0.012 0.001 PHE A 34 TYR 0.011 0.001 TYR A 35 ARG 0.005 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04584 ( 239) hydrogen bonds : angle 3.40119 ( 714) covalent geometry : bond 0.00324 ( 3265) covalent geometry : angle 0.66597 ( 4480) Misc. bond : bond 0.00027 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1685.99 seconds wall clock time: 29 minutes 43.05 seconds (1783.05 seconds total)