Starting phenix.real_space_refine on Tue Feb 11 10:26:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8inb_35595/02_2025/8inb_35595_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8inb_35595/02_2025/8inb_35595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8inb_35595/02_2025/8inb_35595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8inb_35595/02_2025/8inb_35595.map" model { file = "/net/cci-nas-00/data/ceres_data/8inb_35595/02_2025/8inb_35595_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8inb_35595/02_2025/8inb_35595_neut.cif" } resolution = 3.1 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= 0.014 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: 5 Type Number sf(0) Gaussians P 65 5.49 5 S 8 5.16 5 C 3141 2.51 5 N 969 2.21 5 O 1138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5321 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3966 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 37, 'TRANS': 460} Chain breaks: 2 Chain: "B" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 753 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 8, 'rna3p_pur': 11, 'rna3p_pyr': 16} Link IDs: {'rna2p': 9, 'rna3p': 26} Chain: "C" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 463 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 139 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 4.65, per 1000 atoms: 0.87 Number of scatterers: 5321 At special positions: 0 Unit cell: (85.8, 90.42, 97.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 P 65 15.00 O 1138 8.00 N 969 7.00 C 3141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 680.3 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 932 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 49.8% alpha, 9.8% beta 19 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.832A pdb=" N GLY A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 99 removed outlier: 4.178A pdb=" N GLU A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 125 through 168 removed outlier: 6.611A pdb=" N LEU A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.782A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.569A pdb=" N ARG A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 367 through 380 removed outlier: 4.291A pdb=" N LYS A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 450 removed outlier: 3.553A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 464 removed outlier: 3.745A pdb=" N GLU A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 558 removed outlier: 4.182A pdb=" N ALA A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 587 removed outlier: 3.503A pdb=" N ARG A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 removed outlier: 3.958A pdb=" N LEU A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA A 639 " --> pdb=" O PHE A 635 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.793A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN A 64 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLN A 68 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TRP A 304 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 420 removed outlier: 5.958A pdb=" N PHE A 401 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN A 418 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA A 399 " --> pdb=" O GLN A 418 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A 384 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY A 385 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL A 595 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 387 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE A 647 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A 594 " --> pdb=" O ILE A 647 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1308 1.33 - 1.45: 1320 1.45 - 1.57: 2804 1.57 - 1.69: 126 1.69 - 1.81: 11 Bond restraints: 5569 Sorted by residual: bond pdb=" O3' DT D -2 " pdb=" P DT D -1 " ideal model delta sigma weight residual 1.607 1.568 0.039 1.50e-02 4.44e+03 6.74e+00 bond pdb=" O3' DT D -1 " pdb=" P DC D 0 " ideal model delta sigma weight residual 1.607 1.578 0.029 1.50e-02 4.44e+03 3.72e+00 bond pdb=" CA GLU A 380 " pdb=" CB GLU A 380 " ideal model delta sigma weight residual 1.527 1.545 -0.019 1.44e-02 4.82e+03 1.67e+00 bond pdb=" CA VAL A 207 " pdb=" C VAL A 207 " ideal model delta sigma weight residual 1.524 1.515 0.010 1.05e-02 9.07e+03 8.25e-01 bond pdb=" CA HIS A 253 " pdb=" CB HIS A 253 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.31e-02 5.83e+03 7.37e-01 ... (remaining 5564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 7616 1.58 - 3.16: 187 3.16 - 4.73: 23 4.73 - 6.31: 4 6.31 - 7.89: 3 Bond angle restraints: 7833 Sorted by residual: angle pdb=" O3' DC D 0 " pdb=" C3' DC D 0 " pdb=" C2' DC D 0 " ideal model delta sigma weight residual 111.50 103.61 7.89 1.50e+00 4.44e-01 2.77e+01 angle pdb=" O3' DT D -1 " pdb=" C3' DT D -1 " pdb=" C2' DT D -1 " ideal model delta sigma weight residual 111.50 104.60 6.90 1.50e+00 4.44e-01 2.11e+01 angle pdb=" C3' DC D 0 " pdb=" C2' DC D 0 " pdb=" C1' DC D 0 " ideal model delta sigma weight residual 101.60 106.69 -5.09 1.50e+00 4.44e-01 1.15e+01 angle pdb=" C3' DT D -1 " pdb=" C2' DT D -1 " pdb=" C1' DT D -1 " ideal model delta sigma weight residual 101.60 106.48 -4.88 1.50e+00 4.44e-01 1.06e+01 angle pdb=" CA GLU A 380 " pdb=" CB GLU A 380 " pdb=" CG GLU A 380 " ideal model delta sigma weight residual 114.10 120.33 -6.23 2.00e+00 2.50e-01 9.71e+00 ... (remaining 7828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 3078 35.58 - 71.16: 291 71.16 - 106.74: 23 106.74 - 142.32: 0 142.32 - 177.89: 1 Dihedral angle restraints: 3393 sinusoidal: 1953 harmonic: 1440 Sorted by residual: dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual 232.00 54.11 177.89 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' G B 11 " pdb=" C1' G B 11 " pdb=" N9 G B 11 " pdb=" C4 G B 11 " ideal model delta sinusoidal sigma weight residual -106.00 -154.63 48.63 1 1.70e+01 3.46e-03 1.13e+01 dihedral pdb=" CG ARG A 115 " pdb=" CD ARG A 115 " pdb=" NE ARG A 115 " pdb=" CZ ARG A 115 " ideal model delta sinusoidal sigma weight residual -180.00 -135.93 -44.07 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 3390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 670 0.037 - 0.073: 163 0.073 - 0.110: 47 0.110 - 0.147: 14 0.147 - 0.184: 4 Chirality restraints: 898 Sorted by residual: chirality pdb=" C3' DT D -1 " pdb=" C4' DT D -1 " pdb=" O3' DT D -1 " pdb=" C2' DT D -1 " both_signs ideal model delta sigma weight residual False -2.66 -2.84 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" C1' DT D -1 " pdb=" O4' DT D -1 " pdb=" C2' DT D -1 " pdb=" N1 DT D -1 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CA ASN A 234 " pdb=" N ASN A 234 " pdb=" C ASN A 234 " pdb=" CB ASN A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 895 not shown) Planarity restraints: 775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 210 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO A 211 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 223 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO A 224 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 224 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 224 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 242 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO A 243 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.031 5.00e-02 4.00e+02 ... (remaining 772 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 990 2.77 - 3.30: 4776 3.30 - 3.83: 9288 3.83 - 4.37: 10863 4.37 - 4.90: 17091 Nonbonded interactions: 43008 Sorted by model distance: nonbonded pdb=" OG SER A 361 " pdb=" O LEU A 640 " model vdw 2.235 3.040 nonbonded pdb=" O PRO A 224 " pdb=" OG SER A 327 " model vdw 2.252 3.040 nonbonded pdb=" OG SER A 105 " pdb=" OG SER A 108 " model vdw 2.278 3.040 nonbonded pdb=" N GLY A 183 " pdb=" O LYS A 187 " model vdw 2.289 3.120 nonbonded pdb=" NH1 ARG A 70 " pdb=" OD1 ASP A 303 " model vdw 2.292 3.120 ... (remaining 43003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.000 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 : 0.003 0.039 5569 Z= 0.187 Angle : 0.589 7.890 7833 Z= 0.334 Chirality : 0.039 0.184 898 Planarity : 0.006 0.066 775 Dihedral : 22.430 177.895 2461 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.24 % Allowed : 27.19 % Favored : 72.58 % 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: 0.01 (0.39), residues: 492 helix: 1.23 (0.36), residues: 216 sheet: -1.34 (0.67), residues: 62 loop : -0.78 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.021 0.002 HIS A 253 PHE 0.006 0.001 PHE A 102 TYR 0.017 0.001 TYR A 432 ARG 0.003 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.486 Fit side-chains REVERT: A 549 ASP cc_start: 0.6896 (m-30) cc_final: 0.6690 (m-30) outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.2989 time to fit residues: 12.3480 Evaluate side-chains 32 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.0010 chunk 49 optimal weight: 2.9990 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS A 383 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.162559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.123256 restraints weight = 6897.046| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.60 r_work: 0.3288 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5569 Z= 0.222 Angle : 0.556 5.664 7833 Z= 0.297 Chirality : 0.038 0.128 898 Planarity : 0.006 0.054 775 Dihedral : 22.990 179.288 1449 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.18 % Allowed : 26.24 % Favored : 72.58 % 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: 0.25 (0.40), residues: 492 helix: 1.69 (0.36), residues: 217 sheet: -1.68 (0.60), residues: 70 loop : -0.77 (0.46), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 249 HIS 0.012 0.001 HIS A 253 PHE 0.009 0.001 PHE A 137 TYR 0.018 0.001 TYR A 432 ARG 0.004 0.000 ARG A 556 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.454 Fit side-chains REVERT: A 549 ASP cc_start: 0.7717 (m-30) cc_final: 0.7213 (m-30) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.2785 time to fit residues: 14.3699 Evaluate side-chains 37 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 547 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.166782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125138 restraints weight = 7060.899| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.80 r_work: 0.3355 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5569 Z= 0.184 Angle : 0.529 5.297 7833 Z= 0.282 Chirality : 0.037 0.124 898 Planarity : 0.005 0.048 775 Dihedral : 22.780 179.282 1449 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.89 % Allowed : 26.24 % Favored : 71.87 % 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: 0.41 (0.40), residues: 492 helix: 1.87 (0.36), residues: 217 sheet: -1.56 (0.62), residues: 69 loop : -0.77 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 249 HIS 0.014 0.001 HIS A 253 PHE 0.008 0.001 PHE A 137 TYR 0.017 0.001 TYR A 432 ARG 0.006 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.562 Fit side-chains REVERT: A 425 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8119 (tt) REVERT: A 549 ASP cc_start: 0.7724 (m-30) cc_final: 0.7253 (m-30) outliers start: 8 outliers final: 4 residues processed: 45 average time/residue: 0.2616 time to fit residues: 14.6088 Evaluate side-chains 39 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 547 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 42 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 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 = 0.3975 r_free = 0.3975 target = 0.165694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123969 restraints weight = 7139.745| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.81 r_work: 0.3353 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5569 Z= 0.192 Angle : 0.528 4.902 7833 Z= 0.280 Chirality : 0.037 0.136 898 Planarity : 0.005 0.046 775 Dihedral : 22.741 179.225 1449 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.84 % Allowed : 26.00 % Favored : 71.16 % 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: 0.50 (0.40), residues: 492 helix: 1.95 (0.36), residues: 217 sheet: -1.55 (0.61), residues: 69 loop : -0.70 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 249 HIS 0.001 0.000 HIS A 253 PHE 0.008 0.001 PHE A 137 TYR 0.017 0.001 TYR A 432 ARG 0.011 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.520 Fit side-chains REVERT: A 425 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8108 (tt) REVERT: A 549 ASP cc_start: 0.7697 (m-30) cc_final: 0.7239 (m-30) outliers start: 12 outliers final: 8 residues processed: 46 average time/residue: 0.2525 time to fit residues: 14.4366 Evaluate side-chains 44 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.161660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119320 restraints weight = 6989.320| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.85 r_work: 0.3292 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5569 Z= 0.323 Angle : 0.599 5.241 7833 Z= 0.315 Chirality : 0.041 0.139 898 Planarity : 0.006 0.048 775 Dihedral : 22.878 179.786 1449 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.07 % Allowed : 24.82 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.39), residues: 492 helix: 1.75 (0.35), residues: 217 sheet: -1.71 (0.58), residues: 71 loop : -0.77 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 552 HIS 0.001 0.001 HIS A 121 PHE 0.011 0.002 PHE A 350 TYR 0.017 0.002 TYR A 432 ARG 0.007 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.488 Fit side-chains REVERT: A 425 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 549 ASP cc_start: 0.7788 (m-30) cc_final: 0.7309 (m-30) outliers start: 13 outliers final: 11 residues processed: 47 average time/residue: 0.2652 time to fit residues: 15.3589 Evaluate side-chains 43 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 633 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.0070 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 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 = 0.3946 r_free = 0.3946 target = 0.164040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.121589 restraints weight = 7072.741| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.90 r_work: 0.3309 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5569 Z= 0.169 Angle : 0.518 4.583 7833 Z= 0.275 Chirality : 0.037 0.125 898 Planarity : 0.005 0.050 775 Dihedral : 22.664 178.801 1449 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.60 % Allowed : 25.06 % Favored : 72.34 % 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: 0.69 (0.40), residues: 492 helix: 2.10 (0.36), residues: 215 sheet: -1.49 (0.60), residues: 68 loop : -0.57 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 249 HIS 0.001 0.000 HIS A 383 PHE 0.008 0.001 PHE A 137 TYR 0.017 0.001 TYR A 432 ARG 0.009 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.479 Fit side-chains REVERT: A 365 THR cc_start: 0.7780 (p) cc_final: 0.7573 (t) REVERT: A 549 ASP cc_start: 0.7707 (m-30) cc_final: 0.7247 (m-30) outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 0.2182 time to fit residues: 13.7933 Evaluate side-chains 44 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 36 optimal weight: 0.0870 overall best weight: 0.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 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 = 0.3996 r_free = 0.3996 target = 0.168142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125038 restraints weight = 7062.772| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.93 r_work: 0.3336 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5569 Z= 0.175 Angle : 0.518 4.622 7833 Z= 0.273 Chirality : 0.037 0.163 898 Planarity : 0.005 0.045 775 Dihedral : 22.553 178.852 1449 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.89 % Allowed : 26.00 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.40), residues: 492 helix: 2.17 (0.36), residues: 215 sheet: -1.39 (0.61), residues: 69 loop : -0.50 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 249 HIS 0.001 0.000 HIS A 383 PHE 0.008 0.001 PHE A 137 TYR 0.017 0.001 TYR A 432 ARG 0.011 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.476 Fit side-chains REVERT: A 544 ARG cc_start: 0.7358 (tpt170) cc_final: 0.6776 (tpp-160) REVERT: A 549 ASP cc_start: 0.7712 (m-30) cc_final: 0.7271 (m-30) outliers start: 8 outliers final: 7 residues processed: 44 average time/residue: 0.2294 time to fit residues: 12.7273 Evaluate side-chains 41 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 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 203 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 = 0.3975 r_free = 0.3975 target = 0.165410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123349 restraints weight = 6978.126| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.79 r_work: 0.3344 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5569 Z= 0.197 Angle : 0.521 5.154 7833 Z= 0.275 Chirality : 0.037 0.160 898 Planarity : 0.005 0.045 775 Dihedral : 22.549 178.447 1449 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.13 % Allowed : 26.24 % Favored : 71.63 % 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: 0.79 (0.40), residues: 492 helix: 2.17 (0.36), residues: 215 sheet: -1.35 (0.61), residues: 69 loop : -0.53 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 249 HIS 0.001 0.000 HIS A 383 PHE 0.009 0.001 PHE A 137 TYR 0.017 0.001 TYR A 432 ARG 0.008 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.510 Fit side-chains REVERT: A 127 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8415 (tt0) REVERT: A 549 ASP cc_start: 0.7710 (m-30) cc_final: 0.7286 (m-30) outliers start: 9 outliers final: 8 residues processed: 42 average time/residue: 0.2515 time to fit residues: 13.1403 Evaluate side-chains 44 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 35 optimal weight: 0.0170 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 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 = 0.3968 r_free = 0.3968 target = 0.164992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123669 restraints weight = 6974.423| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.75 r_work: 0.3371 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5569 Z= 0.179 Angle : 0.517 5.312 7833 Z= 0.273 Chirality : 0.037 0.173 898 Planarity : 0.005 0.045 775 Dihedral : 22.550 178.431 1449 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.60 % Allowed : 26.00 % Favored : 71.39 % 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: 0.82 (0.40), residues: 492 helix: 2.19 (0.36), residues: 215 sheet: -1.32 (0.61), residues: 69 loop : -0.51 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 249 HIS 0.001 0.000 HIS A 253 PHE 0.008 0.001 PHE A 137 TYR 0.017 0.001 TYR A 432 ARG 0.007 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.526 Fit side-chains REVERT: A 127 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: A 302 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8335 (ttmm) REVERT: A 549 ASP cc_start: 0.7670 (m-30) cc_final: 0.7251 (m-30) outliers start: 11 outliers final: 9 residues processed: 43 average time/residue: 0.2560 time to fit residues: 13.6593 Evaluate side-chains 46 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 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 = 0.3979 r_free = 0.3979 target = 0.165773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123680 restraints weight = 7015.197| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.81 r_work: 0.3346 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5569 Z= 0.184 Angle : 0.516 5.577 7833 Z= 0.273 Chirality : 0.037 0.189 898 Planarity : 0.005 0.045 775 Dihedral : 22.544 178.415 1449 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.60 % Allowed : 25.77 % Favored : 71.63 % 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: 0.83 (0.40), residues: 492 helix: 2.19 (0.36), residues: 215 sheet: -1.31 (0.61), residues: 69 loop : -0.50 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 249 HIS 0.001 0.000 HIS A 383 PHE 0.008 0.001 PHE A 137 TYR 0.017 0.001 TYR A 432 ARG 0.007 0.000 ARG A 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.478 Fit side-chains REVERT: A 127 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8398 (tt0) REVERT: A 302 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8342 (ttmm) REVERT: A 544 ARG cc_start: 0.7383 (tpt170) cc_final: 0.6785 (tpp-160) REVERT: A 549 ASP cc_start: 0.7708 (m-30) cc_final: 0.7279 (m-30) outliers start: 11 outliers final: 9 residues processed: 43 average time/residue: 0.2541 time to fit residues: 13.6745 Evaluate side-chains 46 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 127 GLN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 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 = 0.3964 r_free = 0.3964 target = 0.164841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121939 restraints weight = 7067.279| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.89 r_work: 0.3296 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5569 Z= 0.254 Angle : 0.546 6.032 7833 Z= 0.288 Chirality : 0.038 0.184 898 Planarity : 0.005 0.045 775 Dihedral : 22.569 178.834 1449 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.07 % Allowed : 25.53 % Favored : 71.39 % 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: 0.71 (0.40), residues: 492 helix: 2.10 (0.36), residues: 215 sheet: -1.38 (0.61), residues: 69 loop : -0.58 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 552 HIS 0.002 0.001 HIS A 121 PHE 0.010 0.001 PHE A 350 TYR 0.015 0.001 TYR A 432 ARG 0.006 0.000 ARG A 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3513.77 seconds wall clock time: 62 minutes 45.16 seconds (3765.16 seconds total)