Starting phenix.real_space_refine on Fri Aug 22 15:46:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8inb_35595/08_2025/8inb_35595_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8inb_35595/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8inb_35595/08_2025/8inb_35595_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8inb_35595/08_2025/8inb_35595_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8inb_35595/08_2025/8inb_35595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8inb_35595/08_2025/8inb_35595.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.67, per 1000 atoms: 0.31 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: 0.55 Conformation dependent library (CDL) restraints added in 155.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.71 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: 0.94 Time building geometry restraints manager: 0.68 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.080 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: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.730 Find NCS groups from input model: 0.020 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.580 ------------------------------------------------------------------------------- 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= 0.145 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG A 235 TYR 0.017 0.001 TYR A 432 PHE 0.006 0.001 PHE A 102 TRP 0.015 0.001 TRP A 436 HIS 0.021 0.002 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5569) covalent geometry : angle 0.58865 ( 7833) hydrogen bonds : bond 0.17295 ( 239) hydrogen bonds : angle 5.71626 ( 632) *********************** 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 : 0.116 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: 0.1395 time to fit residues: 5.6279 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 : 0.121 ------------------------------------------------------------------------------- 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 24 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.163507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123971 restraints weight = 7002.173| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.72 r_work: 0.3298 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.0845 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= 0.144 Angle : 0.543 5.646 7833 Z= 0.290 Chirality : 0.038 0.128 898 Planarity : 0.006 0.053 775 Dihedral : 22.975 178.970 1449 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.40), residues: 492 helix: 1.74 (0.36), residues: 217 sheet: -1.66 (0.60), residues: 70 loop : -0.75 (0.46), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 556 TYR 0.018 0.001 TYR A 432 PHE 0.009 0.001 PHE A 137 TRP 0.011 0.001 TRP A 249 HIS 0.013 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 5569) covalent geometry : angle 0.54292 ( 7833) hydrogen bonds : bond 0.04224 ( 239) hydrogen bonds : angle 4.05156 ( 632) *********************** 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 : 0.206 Fit side-chains REVERT: A 549 ASP cc_start: 0.7714 (m-30) cc_final: 0.7206 (m-30) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.1338 time to fit residues: 6.7919 Evaluate side-chains 38 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 51 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.165428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123400 restraints weight = 6952.494| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.84 r_work: 0.3332 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1076 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= 0.145 Angle : 0.539 5.252 7833 Z= 0.286 Chirality : 0.038 0.137 898 Planarity : 0.005 0.048 775 Dihedral : 22.840 179.411 1449 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.42 % Allowed : 26.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.40), residues: 492 helix: 1.83 (0.36), residues: 217 sheet: -1.57 (0.61), residues: 69 loop : -0.79 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 70 TYR 0.017 0.001 TYR A 432 PHE 0.008 0.001 PHE A 350 TRP 0.010 0.001 TRP A 249 HIS 0.001 0.000 HIS A 632 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5569) covalent geometry : angle 0.53946 ( 7833) hydrogen bonds : bond 0.03955 ( 239) hydrogen bonds : angle 3.86345 ( 632) *********************** 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 44 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.185 Fit side-chains REVERT: A 549 ASP cc_start: 0.7744 (m-30) cc_final: 0.7267 (m-30) outliers start: 6 outliers final: 2 residues processed: 43 average time/residue: 0.1308 time to fit residues: 6.8770 Evaluate side-chains 36 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 HIS 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 24 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.158667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116885 restraints weight = 7041.880| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.82 r_work: 0.3284 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 5569 Z= 0.285 Angle : 0.658 5.929 7833 Z= 0.346 Chirality : 0.043 0.139 898 Planarity : 0.006 0.051 775 Dihedral : 23.038 179.432 1449 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.02 % Allowed : 24.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.39), residues: 492 helix: 1.54 (0.35), residues: 217 sheet: -1.75 (0.58), residues: 71 loop : -0.94 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 70 TYR 0.017 0.002 TYR A 432 PHE 0.013 0.002 PHE A 350 TRP 0.012 0.002 TRP A 249 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00661 ( 5569) covalent geometry : angle 0.65754 ( 7833) hydrogen bonds : bond 0.04969 ( 239) hydrogen bonds : angle 4.14644 ( 632) *********************** 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 53 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 36 time to evaluate : 0.184 Fit side-chains REVERT: A 425 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8319 (tt) REVERT: A 545 LYS cc_start: 0.7203 (tptt) cc_final: 0.6773 (mttp) REVERT: A 549 ASP cc_start: 0.7806 (m-30) cc_final: 0.7361 (m-30) outliers start: 17 outliers final: 11 residues processed: 51 average time/residue: 0.1242 time to fit residues: 7.6327 Evaluate side-chains 44 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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 347 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU 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 46 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.0370 chunk 5 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 overall best weight: 0.8060 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.162911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119394 restraints weight = 7170.954| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.98 r_work: 0.3268 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1531 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= 0.150 Angle : 0.550 5.219 7833 Z= 0.290 Chirality : 0.038 0.127 898 Planarity : 0.005 0.048 775 Dihedral : 22.825 179.661 1449 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.89 % Allowed : 25.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.39), residues: 492 helix: 1.82 (0.36), residues: 217 sheet: -1.62 (0.60), residues: 69 loop : -0.79 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.018 0.001 TYR A 432 PHE 0.009 0.001 PHE A 137 TRP 0.013 0.001 TRP A 249 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 5569) covalent geometry : angle 0.55008 ( 7833) hydrogen bonds : bond 0.03980 ( 239) hydrogen bonds : angle 3.85240 ( 632) *********************** 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 44 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.108 Fit side-chains REVERT: A 549 ASP cc_start: 0.7772 (m-30) cc_final: 0.7235 (m-30) outliers start: 8 outliers final: 7 residues processed: 43 average time/residue: 0.1183 time to fit residues: 6.2377 Evaluate side-chains 37 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP 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 439 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.160456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117660 restraints weight = 7107.341| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.90 r_work: 0.3257 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5569 Z= 0.185 Angle : 0.571 5.067 7833 Z= 0.301 Chirality : 0.039 0.156 898 Planarity : 0.005 0.047 775 Dihedral : 22.808 179.973 1449 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.31 % Allowed : 25.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.39), residues: 492 helix: 1.86 (0.36), residues: 215 sheet: -1.66 (0.58), residues: 71 loop : -0.65 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 70 TYR 0.017 0.002 TYR A 432 PHE 0.009 0.001 PHE A 137 TRP 0.012 0.001 TRP A 249 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 5569) covalent geometry : angle 0.57121 ( 7833) hydrogen bonds : bond 0.04135 ( 239) hydrogen bonds : angle 3.85845 ( 632) *********************** 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 47 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.211 Fit side-chains REVERT: A 302 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8347 (ttmm) REVERT: A 372 GLU cc_start: 0.8594 (tp30) cc_final: 0.8328 (tp30) REVERT: A 416 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7687 (mp) REVERT: A 549 ASP cc_start: 0.7760 (m-30) cc_final: 0.7218 (m-30) outliers start: 14 outliers final: 10 residues processed: 46 average time/residue: 0.1090 time to fit residues: 6.1411 Evaluate side-chains 44 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 32 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 222 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 416 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.162979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119663 restraints weight = 7177.000| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.92 r_work: 0.3267 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5569 Z= 0.207 Angle : 0.586 5.177 7833 Z= 0.308 Chirality : 0.040 0.144 898 Planarity : 0.006 0.047 775 Dihedral : 22.806 179.900 1449 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 4.02 % Allowed : 25.06 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.39), residues: 492 helix: 1.84 (0.36), residues: 215 sheet: -1.69 (0.58), residues: 71 loop : -0.68 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 70 TYR 0.017 0.002 TYR A 432 PHE 0.011 0.002 PHE A 137 TRP 0.012 0.002 TRP A 249 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 5569) covalent geometry : angle 0.58598 ( 7833) hydrogen bonds : bond 0.04292 ( 239) hydrogen bonds : angle 3.88836 ( 632) *********************** 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 49 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 0.178 Fit side-chains REVERT: A 302 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8302 (ttmm) REVERT: A 372 GLU cc_start: 0.8542 (tp30) cc_final: 0.8252 (tp30) REVERT: A 416 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7726 (mp) REVERT: A 549 ASP cc_start: 0.7779 (m-30) cc_final: 0.7245 (m-30) outliers start: 17 outliers final: 12 residues processed: 45 average time/residue: 0.1200 time to fit residues: 6.6379 Evaluate side-chains 46 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 222 VAL Chi-restraints excluded: chain A residue 253 HIS 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 359 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 416 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.167537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.124885 restraints weight = 7099.793| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.89 r_work: 0.3339 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1843 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= 0.122 Angle : 0.519 4.862 7833 Z= 0.275 Chirality : 0.037 0.154 898 Planarity : 0.005 0.046 775 Dihedral : 22.597 178.719 1447 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.18 % Allowed : 27.90 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.40), residues: 492 helix: 2.11 (0.36), residues: 215 sheet: -1.29 (0.62), residues: 70 loop : -0.52 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 70 TYR 0.018 0.001 TYR A 432 PHE 0.008 0.001 PHE A 137 TRP 0.014 0.001 TRP A 318 HIS 0.007 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 5569) covalent geometry : angle 0.51878 ( 7833) hydrogen bonds : bond 0.03541 ( 239) hydrogen bonds : angle 3.58493 ( 632) *********************** 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 42 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.183 Fit side-chains REVERT: A 372 GLU cc_start: 0.8489 (tp30) cc_final: 0.8210 (tp30) REVERT: A 549 ASP cc_start: 0.7689 (m-30) cc_final: 0.7236 (m-30) outliers start: 5 outliers final: 5 residues processed: 41 average time/residue: 0.1144 time to fit residues: 5.6842 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 : 0.182 ------------------------------------------------------------------------------- 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 386 LEU Chi-restraints excluded: chain A residue 439 THR 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 47 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.165724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.122826 restraints weight = 7071.076| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.90 r_work: 0.3314 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1847 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= 0.152 Angle : 0.543 5.492 7833 Z= 0.286 Chirality : 0.038 0.177 898 Planarity : 0.005 0.047 775 Dihedral : 22.592 179.134 1447 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.65 % Allowed : 27.66 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.40), residues: 492 helix: 2.06 (0.36), residues: 215 sheet: -1.30 (0.62), residues: 68 loop : -0.53 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 70 TYR 0.017 0.001 TYR A 432 PHE 0.009 0.001 PHE A 137 TRP 0.011 0.001 TRP A 249 HIS 0.004 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 5569) covalent geometry : angle 0.54291 ( 7833) hydrogen bonds : bond 0.03739 ( 239) hydrogen bonds : angle 3.61485 ( 632) *********************** 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 43 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.172 Fit side-chains REVERT: A 372 GLU cc_start: 0.8494 (tp30) cc_final: 0.8203 (tp30) REVERT: A 549 ASP cc_start: 0.7705 (m-30) cc_final: 0.7245 (m-30) outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 0.1240 time to fit residues: 6.3612 Evaluate side-chains 40 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 386 LEU Chi-restraints excluded: chain A residue 439 THR 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 9 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3966 r_free = 0.3966 target = 0.165280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122272 restraints weight = 7171.179| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.91 r_work: 0.3304 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5569 Z= 0.161 Angle : 0.546 5.980 7833 Z= 0.289 Chirality : 0.038 0.186 898 Planarity : 0.005 0.047 775 Dihedral : 22.593 178.998 1447 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.42 % Allowed : 28.13 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.40), residues: 492 helix: 2.03 (0.36), residues: 215 sheet: -1.23 (0.61), residues: 70 loop : -0.51 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 70 TYR 0.017 0.001 TYR A 432 PHE 0.009 0.001 PHE A 137 TRP 0.012 0.001 TRP A 249 HIS 0.002 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5569) covalent geometry : angle 0.54627 ( 7833) hydrogen bonds : bond 0.03804 ( 239) hydrogen bonds : angle 3.64343 ( 632) ********************** 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 41 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.194 Fit side-chains REVERT: A 372 GLU cc_start: 0.8509 (tp30) cc_final: 0.8222 (tp30) REVERT: A 549 ASP cc_start: 0.7735 (m-30) cc_final: 0.7212 (m-30) outliers start: 6 outliers final: 6 residues processed: 40 average time/residue: 0.1393 time to fit residues: 6.7145 Evaluate side-chains 40 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 222 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 439 THR 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 42 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.166384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123326 restraints weight = 7141.788| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.91 r_work: 0.3316 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1946 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= 0.144 Angle : 0.534 5.386 7833 Z= 0.282 Chirality : 0.037 0.180 898 Planarity : 0.005 0.047 775 Dihedral : 22.503 178.574 1447 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.13 % Allowed : 27.19 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.40), residues: 492 helix: 2.09 (0.36), residues: 215 sheet: -1.16 (0.62), residues: 69 loop : -0.53 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 70 TYR 0.017 0.001 TYR A 432 PHE 0.009 0.001 PHE A 137 TRP 0.012 0.001 TRP A 249 HIS 0.003 0.001 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5569) covalent geometry : angle 0.53390 ( 7833) hydrogen bonds : bond 0.03692 ( 239) hydrogen bonds : angle 3.58006 ( 632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1688.00 seconds wall clock time: 29 minutes 32.04 seconds (1772.04 seconds total)