Starting phenix.real_space_refine on Thu Jul 2 01:24:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8inb_35595/07_2026/8inb_35595_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8inb_35595/07_2026/8inb_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_35595/07_2026/8inb_35595_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8inb_35595/07_2026/8inb_35595_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8inb_35595/07_2026/8inb_35595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8inb_35595/07_2026/8inb_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-dev-6108/lib/python3.11/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: 1.36, per 1000 atoms: 0.26 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: 0.40 Conformation dependent library (CDL) restraints added in 143.2 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: 0.42 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: 0.74 Time building geometry restraints manager: 0.47 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=" C3' DC C -14 " pdb=" C2' DC C -14 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.14e+00 bond pdb=" C3' DG C 5 " pdb=" C2' DG C 5 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.51e+00 bond pdb=" O4' DG C -5 " pdb=" C1' DG C -5 " ideal model delta sigma weight residual 1.420 1.399 0.021 1.10e-02 8.26e+03 3.81e+00 bond pdb=" C3' DA C -1 " pdb=" O3' DA C -1 " ideal model delta sigma weight residual 1.435 1.410 0.025 1.30e-02 5.92e+03 3.77e+00 ... (remaining 5564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 7517 1.40 - 2.80: 267 2.80 - 4.19: 43 4.19 - 5.59: 3 5.59 - 6.99: 3 Bond angle restraints: 7833 Sorted by residual: angle pdb=" N3 DT C -7 " pdb=" C4 DT C -7 " pdb=" O4 DT C -7 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT C 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT D -2 " pdb=" C4 DT D -2 " pdb=" O4 DT D -2 " ideal model delta sigma weight residual 119.90 122.28 -2.38 6.00e-01 2.78e+00 1.58e+01 angle pdb=" O4 DT C -7 " pdb=" C4 DT C -7 " pdb=" C5 DT C -7 " ideal model delta sigma weight residual 124.90 122.18 2.72 7.00e-01 2.04e+00 1.51e+01 ... (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 - 0.032: 586 0.032 - 0.063: 208 0.063 - 0.095: 61 0.095 - 0.126: 38 0.126 - 0.158: 5 Chirality restraints: 898 Sorted by residual: 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 chirality pdb=" CA ILE A 419 " pdb=" N ILE A 419 " pdb=" C ILE A 419 " pdb=" CB ILE A 419 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.05e-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 2.43 2.30 0.13 2.00e-01 2.50e+01 4.14e-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: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.150 Find NCS groups from input model: 0.010 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.004 0.039 5569 Z= 0.263 Angle : 0.615 6.988 7833 Z= 0.457 Chirality : 0.041 0.158 898 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 are 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/Z covalent geometry : bond 0.00354 / 0.26 ( 5569) covalent geometry : angle 0.61478 / 0.46 ( 7833) hydrogen bonds : bond 0.17295 / 10.96 ( 239) hydrogen bonds : angle 5.71626 / 4.04 ( 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 : 0.159 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: 0.1238 time to fit residues: 5.1274 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 : 0.159 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3904 r_free = 0.3904 target = 0.163336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124278 restraints weight = 7004.447| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.69 r_work: 0.3300 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0646 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= 0.145 Angle : 0.549 5.767 7833 Z= 0.310 Chirality : 0.040 0.147 898 Planarity : 0.006 0.061 775 Dihedral : 23.081 179.694 1449 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.42 % Allowed : 26.00 % 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 are not related in a simple way. whole: 0.24 (0.40), residues: 492 helix: 1.58 (0.36), residues: 217 sheet: -1.36 (0.63), residues: 64 loop : -0.82 (0.45), residues: 211 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 0.011 0.001 PHE A 350 TRP 0.011 0.001 TRP A 249 HIS 0.016 0.002 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 ( 5569) covalent geometry : angle 0.54929 / 0.31 ( 7833) hydrogen bonds : bond 0.05155 / 3.32 ( 239) hydrogen bonds : angle 4.24482 / 3.13 ( 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 43 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.154 Fit side-chains REVERT: A 549 ASP cc_start: 0.7720 (m-30) cc_final: 0.7236 (m-30) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.1133 time to fit residues: 5.8767 Evaluate side-chains 39 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 565 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 12 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3879 r_free = 0.3879 target = 0.161081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122224 restraints weight = 6935.834| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.65 r_work: 0.3270 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.0940 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= 0.183 Angle : 0.568 5.538 7833 Z= 0.315 Chirality : 0.041 0.150 898 Planarity : 0.006 0.050 775 Dihedral : 23.070 179.949 1449 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 1.42 % Allowed : 26.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.39), residues: 492 helix: 1.67 (0.36), residues: 217 sheet: -1.64 (0.59), residues: 70 loop : -0.81 (0.46), residues: 205 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 0.010 0.001 PHE A 102 TRP 0.012 0.002 TRP A 249 HIS 0.016 0.002 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 5569) covalent geometry : angle 0.56833 / 0.31 ( 7833) hydrogen bonds : bond 0.04749 / 3.15 ( 239) hydrogen bonds : angle 4.07977 / 3.02 ( 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 43 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.112 Fit side-chains REVERT: A 234 ASN cc_start: 0.7987 (p0) cc_final: 0.7778 (p0) REVERT: A 549 ASP cc_start: 0.7705 (m-30) cc_final: 0.7203 (m-30) outliers start: 6 outliers final: 2 residues processed: 43 average time/residue: 0.1317 time to fit residues: 6.7883 Evaluate side-chains 37 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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: 0.9990 chunk 53 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 22 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 30 optimal weight: 0.0970 chunk 45 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3984 r_free = 0.3984 target = 0.166360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124729 restraints weight = 7078.149| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.80 r_work: 0.3353 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5569 Z= 0.117 Angle : 0.508 5.021 7833 Z= 0.283 Chirality : 0.038 0.147 898 Planarity : 0.005 0.046 775 Dihedral : 23.002 179.226 1449 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.13 % Allowed : 26.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.39), residues: 492 helix: 1.88 (0.36), residues: 217 sheet: -1.39 (0.61), residues: 69 loop : -0.74 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 70 TYR 0.019 0.001 TYR A 432 PHE 0.008 0.001 PHE A 137 TRP 0.011 0.001 TRP A 249 HIS 0.001 0.000 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 ( 5569) covalent geometry : angle 0.50753 / 0.28 ( 7833) hydrogen bonds : bond 0.03969 / 2.63 ( 239) hydrogen bonds : angle 3.83415 / 2.82 ( 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 51 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.174 Fit side-chains REVERT: A 234 ASN cc_start: 0.8057 (p0) cc_final: 0.7843 (p0) REVERT: A 549 ASP cc_start: 0.7713 (m-30) cc_final: 0.7213 (m-30) outliers start: 9 outliers final: 7 residues processed: 48 average time/residue: 0.1173 time to fit residues: 6.8586 Evaluate side-chains 45 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP 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 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: 0.9980 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 11 optimal weight: 20.0000 chunk 12 optimal weight: 0.2980 chunk 53 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3978 r_free = 0.3978 target = 0.165823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124082 restraints weight = 7151.580| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.82 r_work: 0.3348 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1234 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= 0.130 Angle : 0.514 5.698 7833 Z= 0.285 Chirality : 0.039 0.153 898 Planarity : 0.005 0.045 775 Dihedral : 22.928 179.350 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 : 2.60 % Allowed : 26.48 % 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 are not related in a simple way. whole: 0.52 (0.39), residues: 492 helix: 1.93 (0.36), residues: 217 sheet: -1.42 (0.60), residues: 69 loop : -0.70 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 70 TYR 0.017 0.001 TYR A 432 PHE 0.009 0.001 PHE A 137 TRP 0.009 0.001 TRP A 249 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 5569) covalent geometry : angle 0.51412 / 0.29 ( 7833) hydrogen bonds : bond 0.03964 / 2.64 ( 239) hydrogen bonds : angle 3.77526 / 2.78 ( 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 48 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.176 Fit side-chains REVERT: A 234 ASN cc_start: 0.8070 (p0) cc_final: 0.7846 (p0) REVERT: A 549 ASP cc_start: 0.7724 (m-30) cc_final: 0.7213 (m-30) outliers start: 11 outliers final: 8 residues processed: 44 average time/residue: 0.1221 time to fit residues: 6.5198 Evaluate side-chains 43 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 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 210 ASN 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: 0.9980 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.165143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123476 restraints weight = 7074.957| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.81 r_work: 0.3341 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5569 Z= 0.140 Angle : 0.516 6.164 7833 Z= 0.286 Chirality : 0.039 0.156 898 Planarity : 0.005 0.057 775 Dihedral : 22.919 179.370 1449 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.36 % Allowed : 26.71 % 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 are not related in a simple way. whole: 0.56 (0.39), residues: 492 helix: 1.96 (0.36), residues: 217 sheet: -1.44 (0.59), residues: 69 loop : -0.67 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 70 TYR 0.017 0.001 TYR A 432 PHE 0.009 0.001 PHE A 137 TRP 0.009 0.001 TRP A 249 HIS 0.001 0.000 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 5569) covalent geometry : angle 0.51564 / 0.29 ( 7833) hydrogen bonds : bond 0.03971 / 2.66 ( 239) hydrogen bonds : angle 3.74774 / 2.76 ( 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 46 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.170 Fit side-chains REVERT: A 234 ASN cc_start: 0.8120 (p0) cc_final: 0.7880 (p0) REVERT: A 549 ASP cc_start: 0.7726 (m-30) cc_final: 0.7209 (m-30) outliers start: 10 outliers final: 10 residues processed: 42 average time/residue: 0.0914 time to fit residues: 4.8912 Evaluate side-chains 45 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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 210 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3953 r_free = 0.3953 target = 0.163612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.121707 restraints weight = 7165.508| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.81 r_work: 0.3308 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5569 Z= 0.174 Angle : 0.549 5.683 7833 Z= 0.301 Chirality : 0.040 0.156 898 Planarity : 0.005 0.046 775 Dihedral : 22.957 179.850 1449 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.31 % Allowed : 26.48 % Favored : 70.21 % 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 are not related in a simple way. whole: 0.47 (0.39), residues: 492 helix: 1.89 (0.36), residues: 217 sheet: -1.59 (0.57), residues: 71 loop : -0.66 (0.46), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 70 TYR 0.016 0.002 TYR A 432 PHE 0.010 0.001 PHE A 137 TRP 0.010 0.001 TRP A 552 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 5569) covalent geometry : angle 0.54937 / 0.30 ( 7833) hydrogen bonds : bond 0.04284 / 2.88 ( 239) hydrogen bonds : angle 3.81017 / 2.82 ( 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 50 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.178 Fit side-chains REVERT: A 234 ASN cc_start: 0.8220 (p0) cc_final: 0.7969 (p0) REVERT: A 549 ASP cc_start: 0.7747 (m-30) cc_final: 0.7223 (m-30) outliers start: 14 outliers final: 11 residues processed: 47 average time/residue: 0.1179 time to fit residues: 6.8981 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 : 0.232 ------------------------------------------------------------------------------- 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 210 ASN Chi-restraints excluded: chain A residue 222 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.165022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123284 restraints weight = 7097.218| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.81 r_work: 0.3331 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1477 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= 0.137 Angle : 0.513 5.567 7833 Z= 0.284 Chirality : 0.039 0.149 898 Planarity : 0.005 0.045 775 Dihedral : 22.938 179.260 1449 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.60 % Allowed : 26.24 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.39), residues: 492 helix: 2.07 (0.36), residues: 215 sheet: -1.44 (0.59), residues: 69 loop : -0.59 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 70 TYR 0.017 0.001 TYR A 432 PHE 0.010 0.001 PHE A 137 TRP 0.013 0.001 TRP A 249 HIS 0.001 0.000 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 5569) covalent geometry : angle 0.51263 / 0.28 ( 7833) hydrogen bonds : bond 0.03942 / 2.66 ( 239) hydrogen bonds : angle 3.68267 / 2.72 ( 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 47 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.176 Fit side-chains REVERT: A 234 ASN cc_start: 0.8254 (p0) cc_final: 0.7993 (p0) REVERT: A 549 ASP cc_start: 0.7716 (m-30) cc_final: 0.7194 (m-30) REVERT: A 554 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8074 (mt) outliers start: 11 outliers final: 10 residues processed: 44 average time/residue: 0.0911 time to fit residues: 5.0601 Evaluate side-chains 45 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 210 ASN 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 554 LEU 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: 0.9980 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.0370 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3939 r_free = 0.3939 target = 0.163338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120959 restraints weight = 7107.012| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.89 r_work: 0.3296 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1553 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= 0.131 Angle : 0.511 5.435 7833 Z= 0.282 Chirality : 0.038 0.144 898 Planarity : 0.005 0.044 775 Dihedral : 22.901 179.325 1449 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.13 % Allowed : 27.66 % Favored : 70.21 % 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 are not related in a simple way. whole: 0.70 (0.39), residues: 492 helix: 2.10 (0.35), residues: 215 sheet: -1.44 (0.60), residues: 68 loop : -0.58 (0.45), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 552 HIS 0.001 0.000 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 5569) covalent geometry : angle 0.51064 / 0.28 ( 7833) hydrogen bonds : bond 0.03876 / 2.62 ( 239) hydrogen bonds : angle 3.62893 / 2.66 ( 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 45 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.181 Fit side-chains REVERT: A 234 ASN cc_start: 0.8260 (p0) cc_final: 0.8001 (p0) REVERT: A 365 THR cc_start: 0.7844 (p) cc_final: 0.7624 (t) REVERT: A 372 GLU cc_start: 0.8576 (tp30) cc_final: 0.8300 (tp30) REVERT: A 549 ASP cc_start: 0.7698 (m-30) cc_final: 0.7164 (m-30) outliers start: 9 outliers final: 9 residues processed: 41 average time/residue: 0.1135 time to fit residues: 5.7619 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 : 0.179 ------------------------------------------------------------------------------- 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 210 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3941 r_free = 0.3941 target = 0.163559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121020 restraints weight = 7196.348| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.92 r_work: 0.3297 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5569 Z= 0.134 Angle : 0.507 5.319 7833 Z= 0.280 Chirality : 0.039 0.179 898 Planarity : 0.005 0.045 775 Dihedral : 22.893 179.043 1449 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.60 % Allowed : 26.95 % 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 are not related in a simple way. whole: 0.76 (0.40), residues: 492 helix: 2.12 (0.35), residues: 215 sheet: -1.32 (0.60), residues: 69 loop : -0.54 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 70 TYR 0.017 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 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 5569) covalent geometry : angle 0.50720 / 0.28 ( 7833) hydrogen bonds : bond 0.03854 / 2.61 ( 239) hydrogen bonds : angle 3.61641 / 2.65 ( 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 47 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.179 Fit side-chains REVERT: A 234 ASN cc_start: 0.8285 (p0) cc_final: 0.8023 (p0) REVERT: A 365 THR cc_start: 0.7830 (p) cc_final: 0.7613 (t) REVERT: A 372 GLU cc_start: 0.8545 (tp30) cc_final: 0.8265 (tp30) REVERT: A 549 ASP cc_start: 0.7722 (m-30) cc_final: 0.7189 (m-30) outliers start: 11 outliers final: 10 residues processed: 44 average time/residue: 0.1200 time to fit residues: 6.5303 Evaluate side-chains 45 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 210 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 chunk 12 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 34 optimal weight: 0.0060 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.165786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123658 restraints weight = 7144.784| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.90 r_work: 0.3336 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5569 Z= 0.109 Angle : 0.493 5.195 7833 Z= 0.273 Chirality : 0.037 0.168 898 Planarity : 0.005 0.044 775 Dihedral : 22.828 178.711 1449 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % 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 are not related in a simple way. whole: 0.89 (0.40), residues: 492 helix: 2.25 (0.36), residues: 215 sheet: -1.25 (0.61), residues: 69 loop : -0.49 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 70 TYR 0.017 0.001 TYR A 432 PHE 0.008 0.001 PHE A 137 TRP 0.013 0.001 TRP A 318 HIS 0.001 0.000 HIS A 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 ( 5569) covalent geometry : angle 0.49344 / 0.27 ( 7833) hydrogen bonds : bond 0.03540 / 2.39 ( 239) hydrogen bonds : angle 3.50079 / 2.55 ( 632) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1778.14 seconds wall clock time: 31 minutes 11.91 seconds (1871.91 seconds total)