Starting phenix.real_space_refine on Wed Jul 1 22:48:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7soc_25266/07_2026/7soc_25266.cif Found real_map, /net/cci-nas-00/data/ceres_data/7soc_25266/07_2026/7soc_25266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7soc_25266/07_2026/7soc_25266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7soc_25266/07_2026/7soc_25266.map" model { file = "/net/cci-nas-00/data/ceres_data/7soc_25266/07_2026/7soc_25266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7soc_25266/07_2026/7soc_25266.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7soc_25266/07_2026/7soc_25266.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7soc_25266/07_2026/7soc_25266.cif" } resolution = 3.3 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= -0.002 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2176 2.51 5 N 577 2.21 5 O 679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 3448 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1589 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 12, 'TRANS': 187} Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 996 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 778 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.92, per 1000 atoms: 0.27 Number of scatterers: 3448 At special positions: 0 Unit cell: (91.887, 78.399, 82.614, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 679 8.00 N 577 7.00 C 2176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.10 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.07 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.07 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 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " BETA1-6 " NAG B 1 " - " FUC B 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG B 1 " - " ASN A 343 " Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 127.4 milliseconds 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 10.9% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.841A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.621A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.152A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.006A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.658A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.604A pdb=" N GLY H 33 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.803A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 11 116 hydrogen bonds defined for protein. 261 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.46 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: 1.20 - 1.33: 930 1.33 - 1.46: 914 1.46 - 1.58: 1671 1.58 - 1.71: 0 1.71 - 1.84: 19 Bond restraints: 3534 Sorted by residual: bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.475 -0.062 2.00e-02 2.50e+03 9.50e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.465 -0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" C5 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.418 1.469 -0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" C5 MAN B 5 " pdb=" O5 MAN B 5 " ideal model delta sigma weight residual 1.418 1.469 -0.051 2.00e-02 2.50e+03 6.50e+00 bond pdb=" N ASP H 115 " pdb=" CA ASP H 115 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.37e+00 ... (remaining 3529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 4088 1.51 - 3.02: 584 3.02 - 4.53: 79 4.53 - 6.04: 34 6.04 - 7.55: 19 Bond angle restraints: 4804 Sorted by residual: angle pdb=" C PHE A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta sigma weight residual 119.56 126.74 -7.18 1.02e+00 9.61e-01 4.95e+01 angle pdb=" C ILE L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 119.89 126.97 -7.08 1.02e+00 9.61e-01 4.82e+01 angle pdb=" C LEU A 425 " pdb=" N PRO A 426 " pdb=" CA PRO A 426 " ideal model delta sigma weight residual 119.85 126.82 -6.97 1.01e+00 9.80e-01 4.76e+01 angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.56 126.57 -7.01 1.02e+00 9.61e-01 4.72e+01 angle pdb=" C THR A 478 " pdb=" N PRO A 479 " pdb=" CA PRO A 479 " ideal model delta sigma weight residual 119.78 126.73 -6.95 1.03e+00 9.43e-01 4.55e+01 ... (remaining 4799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 1930 15.39 - 30.77: 65 30.77 - 46.16: 11 46.16 - 61.54: 9 61.54 - 76.93: 6 Dihedral angle restraints: 2021 sinusoidal: 782 harmonic: 1239 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 122.21 -29.21 1 1.00e+01 1.00e-02 1.22e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 65.98 27.02 1 1.00e+01 1.00e-02 1.05e+01 dihedral pdb=" CA ASP H 99 " pdb=" CB ASP H 99 " pdb=" CG ASP H 99 " pdb=" OD1 ASP H 99 " ideal model delta sinusoidal sigma weight residual -30.00 -78.15 48.15 1 2.00e+01 2.50e-03 7.99e+00 ... (remaining 2018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 414 0.075 - 0.150: 95 0.150 - 0.225: 21 0.225 - 0.299: 3 0.299 - 0.374: 3 Chirality restraints: 536 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.01e+02 chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.16e+01 chirality pdb=" C1 MAN B 4 " pdb=" O3 BMA B 3 " pdb=" C2 MAN B 4 " pdb=" O5 MAN B 4 " both_signs ideal model delta sigma weight residual False 2.40 2.46 -0.06 2.00e-02 2.50e+03 9.33e+00 ... (remaining 533 not shown) Planarity restraints: 614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY H 113 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C GLY H 113 " -0.051 2.00e-02 2.50e+03 pdb=" O GLY H 113 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE H 114 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.023 2.00e-02 2.50e+03 2.30e-02 6.62e+00 pdb=" CG ASN A 331 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.034 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 382 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C VAL A 382 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL A 382 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS A 383 " -0.012 2.00e-02 2.50e+03 ... (remaining 611 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 1858 3.00 - 3.48: 2935 3.48 - 3.95: 5779 3.95 - 4.43: 6532 4.43 - 4.90: 10740 Nonbonded interactions: 27844 Sorted by model distance: nonbonded pdb=" N ASP H 115 " pdb=" OD1 ASP H 115 " model vdw 2.526 3.120 nonbonded pdb=" N ASP L 61 " pdb=" OD1 ASP L 61 " model vdw 2.528 3.120 nonbonded pdb=" N ASP A 428 " pdb=" OD1 ASP A 428 " model vdw 2.592 3.120 nonbonded pdb=" N ASP H 89 " pdb=" OD1 ASP H 89 " model vdw 2.598 3.120 nonbonded pdb=" N GLU L 80 " pdb=" O GLU L 80 " model vdw 2.607 2.496 ... (remaining 27839 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: 9.540 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.140 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: 15.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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 : 0.011 0.070 3547 Z= 0.613 Angle : 1.235 7.554 4837 Z= 0.816 Chirality : 0.072 0.374 536 Planarity : 0.005 0.029 612 Dihedral : 10.609 76.926 1221 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.30 (0.39), residues: 427 helix: -4.85 (0.23), residues: 27 sheet: 0.86 (0.41), residues: 154 loop : 0.50 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.023 0.003 TYR A 495 PHE 0.032 0.003 PHE A 329 TRP 0.020 0.004 TRP H 50 HIS 0.002 0.001 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01090 / 0.60 ( 3534) covalent geometry : angle 1.22105 / 0.81 ( 4804) SS BOND : bond 0.03812 / 1.82 ( 6) SS BOND : angle 3.15232 / 1.92 ( 12) hydrogen bonds : bond 0.16523 / 10.21 ( 113) hydrogen bonds : angle 8.98908 / 6.35 ( 261) link_ALPHA1-3 : bond 0.06203 / 3.26 ( 1) link_ALPHA1-3 : angle 2.04188 / 1.10 ( 3) link_ALPHA1-6 : bond 0.05231 / 2.75 ( 1) link_ALPHA1-6 : angle 2.56792 / 1.59 ( 3) link_BETA1-4 : bond 0.06420 / 3.24 ( 2) link_BETA1-4 : angle 2.17920 / 1.25 ( 6) link_BETA1-6 : bond 0.04396 / 2.31 ( 1) link_BETA1-6 : angle 1.49948 / 0.85 ( 3) link_NAG-ASN : bond 0.05479 / 2.74 ( 2) link_NAG-ASN : angle 1.92623 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.127 Fit side-chains REVERT: A 340 GLU cc_start: 0.8715 (pt0) cc_final: 0.8477 (pt0) REVERT: A 378 LYS cc_start: 0.8603 (mttt) cc_final: 0.8141 (mtmt) REVERT: A 406 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7994 (mt-10) REVERT: A 517 LEU cc_start: 0.6915 (tp) cc_final: 0.6336 (tp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.0675 time to fit residues: 4.6496 Evaluate side-chains 35 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.0870 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.0980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.112529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.098576 restraints weight = 4196.197| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.30 r_work: 0.2858 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3547 Z= 0.138 Angle : 0.519 5.181 4837 Z= 0.277 Chirality : 0.044 0.174 536 Planarity : 0.004 0.033 612 Dihedral : 4.024 12.359 480 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.10 % Allowed : 5.23 % Favored : 93.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.43 (0.40), residues: 427 helix: -4.30 (0.46), residues: 27 sheet: 0.77 (0.40), residues: 158 loop : 0.67 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.017 0.001 TYR A 495 PHE 0.019 0.002 PHE A 515 TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 3534) covalent geometry : angle 0.50453 / 0.27 ( 4804) SS BOND : bond 0.00447 / 0.21 ( 6) SS BOND : angle 1.02115 / 0.56 ( 12) hydrogen bonds : bond 0.04073 / 2.49 ( 113) hydrogen bonds : angle 7.11717 / 5.00 ( 261) link_ALPHA1-3 : bond 0.00947 / 0.50 ( 1) link_ALPHA1-3 : angle 1.52909 / 1.18 ( 3) link_ALPHA1-6 : bond 0.00923 / 0.49 ( 1) link_ALPHA1-6 : angle 1.52122 / 1.12 ( 3) link_BETA1-4 : bond 0.00801 / 0.40 ( 2) link_BETA1-4 : angle 2.19668 / 1.63 ( 6) link_BETA1-6 : bond 0.00470 / 0.25 ( 1) link_BETA1-6 : angle 1.22298 / 0.88 ( 3) link_NAG-ASN : bond 0.00692 / 0.35 ( 2) link_NAG-ASN : angle 1.77623 / 1.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.157 Fit side-chains REVERT: A 340 GLU cc_start: 0.8797 (pt0) cc_final: 0.8571 (pt0) REVERT: A 378 LYS cc_start: 0.8775 (mttt) cc_final: 0.8009 (mtmt) REVERT: A 471 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7987 (mt-10) REVERT: H 102 ARG cc_start: 0.9292 (ttm-80) cc_final: 0.8899 (ttm-80) outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 0.0566 time to fit residues: 2.9408 Evaluate side-chains 34 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 69 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 20 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.111597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.097026 restraints weight = 4189.708| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.36 r_work: 0.2832 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3547 Z= 0.167 Angle : 0.518 6.021 4837 Z= 0.271 Chirality : 0.045 0.163 536 Planarity : 0.005 0.034 612 Dihedral : 3.913 12.993 480 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.65 % Allowed : 6.06 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.32 (0.41), residues: 427 helix: -4.12 (0.56), residues: 27 sheet: 0.67 (0.40), residues: 158 loop : 0.57 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.022 0.002 TYR A 495 PHE 0.014 0.002 PHE A 429 TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 3534) covalent geometry : angle 0.50756 / 0.27 ( 4804) SS BOND : bond 0.00383 / 0.21 ( 6) SS BOND : angle 0.93791 / 0.51 ( 12) hydrogen bonds : bond 0.03718 / 2.27 ( 113) hydrogen bonds : angle 6.68289 / 4.74 ( 261) link_ALPHA1-3 : bond 0.00661 / 0.35 ( 1) link_ALPHA1-3 : angle 1.36610 / 1.10 ( 3) link_ALPHA1-6 : bond 0.00749 / 0.39 ( 1) link_ALPHA1-6 : angle 1.23348 / 0.92 ( 3) link_BETA1-4 : bond 0.00671 / 0.33 ( 2) link_BETA1-4 : angle 1.75211 / 1.21 ( 6) link_BETA1-6 : bond 0.00341 / 0.18 ( 1) link_BETA1-6 : angle 1.12237 / 0.77 ( 3) link_NAG-ASN : bond 0.00546 / 0.29 ( 2) link_NAG-ASN : angle 1.68485 / 1.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.101 Fit side-chains REVERT: A 378 LYS cc_start: 0.8834 (mttt) cc_final: 0.8069 (mtmt) REVERT: A 471 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8180 (mt-10) REVERT: H 102 ARG cc_start: 0.9320 (ttm-80) cc_final: 0.9080 (ttm-80) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.0476 time to fit residues: 2.6243 Evaluate side-chains 35 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.110087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.095393 restraints weight = 4123.648| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.37 r_work: 0.2805 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3547 Z= 0.191 Angle : 0.544 8.693 4837 Z= 0.275 Chirality : 0.047 0.378 536 Planarity : 0.005 0.037 612 Dihedral : 4.012 13.466 480 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.20 % Allowed : 6.61 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.17 (0.41), residues: 427 helix: -3.97 (0.67), residues: 27 sheet: 0.53 (0.40), residues: 158 loop : 0.47 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.019 0.002 TYR A 495 PHE 0.009 0.002 PHE L 84 TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 3534) covalent geometry : angle 0.51891 / 0.27 ( 4804) SS BOND : bond 0.00379 / 0.19 ( 6) SS BOND : angle 0.79527 / 0.44 ( 12) hydrogen bonds : bond 0.03616 / 2.23 ( 113) hydrogen bonds : angle 6.57950 / 4.64 ( 261) link_ALPHA1-3 : bond 0.00694 / 0.37 ( 1) link_ALPHA1-3 : angle 1.36892 / 1.13 ( 3) link_ALPHA1-6 : bond 0.00767 / 0.40 ( 1) link_ALPHA1-6 : angle 1.26902 / 0.97 ( 3) link_BETA1-4 : bond 0.00615 / 0.30 ( 2) link_BETA1-4 : angle 1.80687 / 1.25 ( 6) link_BETA1-6 : bond 0.00277 / 0.15 ( 1) link_BETA1-6 : angle 1.19299 / 0.84 ( 3) link_NAG-ASN : bond 0.01214 / 0.64 ( 2) link_NAG-ASN : angle 3.96244 / 2.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.134 Fit side-chains REVERT: A 378 LYS cc_start: 0.8818 (mttt) cc_final: 0.8134 (mtmt) REVERT: A 471 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8194 (mt-10) REVERT: H 70 MET cc_start: 0.9324 (mtt) cc_final: 0.8706 (mtt) REVERT: L 82 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7880 (pm20) outliers start: 8 outliers final: 7 residues processed: 35 average time/residue: 0.0319 time to fit residues: 1.7050 Evaluate side-chains 37 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 15 optimal weight: 0.0670 chunk 22 optimal weight: 0.0770 chunk 33 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.111439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.095602 restraints weight = 4145.607| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.48 r_work: 0.2807 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3547 Z= 0.128 Angle : 0.492 8.218 4837 Z= 0.247 Chirality : 0.044 0.279 536 Planarity : 0.004 0.036 612 Dihedral : 3.804 13.741 480 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.55 % Allowed : 8.82 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.21 (0.41), residues: 427 helix: -3.99 (0.67), residues: 27 sheet: 0.53 (0.41), residues: 158 loop : 0.53 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.012 0.001 TYR A 495 PHE 0.007 0.001 PHE L 84 TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 3534) covalent geometry : angle 0.46248 / 0.24 ( 4804) SS BOND : bond 0.00267 / 0.13 ( 6) SS BOND : angle 0.61559 / 0.35 ( 12) hydrogen bonds : bond 0.03184 / 1.95 ( 113) hydrogen bonds : angle 6.32331 / 4.44 ( 261) link_ALPHA1-3 : bond 0.00733 / 0.39 ( 1) link_ALPHA1-3 : angle 1.33539 / 1.10 ( 3) link_ALPHA1-6 : bond 0.00777 / 0.41 ( 1) link_ALPHA1-6 : angle 1.25820 / 0.99 ( 3) link_BETA1-4 : bond 0.00591 / 0.29 ( 2) link_BETA1-4 : angle 1.60570 / 1.14 ( 6) link_BETA1-6 : bond 0.00241 / 0.13 ( 1) link_BETA1-6 : angle 1.19730 / 0.90 ( 3) link_NAG-ASN : bond 0.00961 / 0.51 ( 2) link_NAG-ASN : angle 4.26723 / 3.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.072 Fit side-chains REVERT: A 378 LYS cc_start: 0.8803 (mttt) cc_final: 0.8119 (mtmt) REVERT: A 471 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8198 (mt-10) REVERT: H 43 GLN cc_start: 0.8623 (mm110) cc_final: 0.8322 (mp10) outliers start: 2 outliers final: 2 residues processed: 34 average time/residue: 0.0328 time to fit residues: 1.5666 Evaluate side-chains 33 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.108910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.094073 restraints weight = 4163.730| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.39 r_work: 0.2784 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 3547 Z= 0.232 Angle : 0.584 7.131 4837 Z= 0.293 Chirality : 0.051 0.464 536 Planarity : 0.005 0.040 612 Dihedral : 4.053 14.306 480 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.20 % Allowed : 7.71 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.05 (0.42), residues: 427 helix: -3.93 (0.69), residues: 27 sheet: 0.27 (0.41), residues: 158 loop : 0.39 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 67 TYR 0.019 0.002 TYR A 495 PHE 0.011 0.002 PHE A 429 TRP 0.012 0.001 TRP H 47 HIS 0.005 0.002 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.23 ( 3534) covalent geometry : angle 0.56135 / 0.29 ( 4804) SS BOND : bond 0.00425 / 0.23 ( 6) SS BOND : angle 0.81235 / 0.46 ( 12) hydrogen bonds : bond 0.03680 / 2.27 ( 113) hydrogen bonds : angle 6.52970 / 4.58 ( 261) link_ALPHA1-3 : bond 0.00618 / 0.33 ( 1) link_ALPHA1-3 : angle 1.40544 / 1.15 ( 3) link_ALPHA1-6 : bond 0.00653 / 0.34 ( 1) link_ALPHA1-6 : angle 1.20336 / 0.92 ( 3) link_BETA1-4 : bond 0.00620 / 0.30 ( 2) link_BETA1-4 : angle 1.88008 / 1.26 ( 6) link_BETA1-6 : bond 0.00227 / 0.12 ( 1) link_BETA1-6 : angle 1.24512 / 0.89 ( 3) link_NAG-ASN : bond 0.01783 / 0.94 ( 2) link_NAG-ASN : angle 3.87160 / 2.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.103 Fit side-chains REVERT: A 378 LYS cc_start: 0.8808 (mttt) cc_final: 0.8125 (mtmt) REVERT: A 471 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8164 (mt-10) REVERT: H 43 GLN cc_start: 0.8541 (mm110) cc_final: 0.8275 (mp10) REVERT: H 70 MET cc_start: 0.9333 (mtt) cc_final: 0.8565 (mtt) REVERT: L 82 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7956 (pm20) outliers start: 8 outliers final: 7 residues processed: 34 average time/residue: 0.0354 time to fit residues: 1.6935 Evaluate side-chains 36 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 12 optimal weight: 0.4980 chunk 0 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.113255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.096003 restraints weight = 4118.618| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.62 r_work: 0.2811 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3547 Z= 0.145 Angle : 0.588 15.931 4837 Z= 0.274 Chirality : 0.044 0.188 536 Planarity : 0.004 0.036 612 Dihedral : 3.892 13.670 480 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.20 % Allowed : 8.82 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.00 (0.42), residues: 427 helix: -3.95 (0.68), residues: 27 sheet: 0.35 (0.41), residues: 158 loop : 0.40 (0.43), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.011 0.001 TYR A 369 PHE 0.007 0.001 PHE H 29 TRP 0.010 0.001 TRP H 47 HIS 0.004 0.001 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 3534) covalent geometry : angle 0.49705 / 0.25 ( 4804) SS BOND : bond 0.00303 / 0.15 ( 6) SS BOND : angle 0.67133 / 0.39 ( 12) hydrogen bonds : bond 0.03268 / 2.01 ( 113) hydrogen bonds : angle 6.34736 / 4.43 ( 261) link_ALPHA1-3 : bond 0.00729 / 0.38 ( 1) link_ALPHA1-3 : angle 1.36235 / 1.12 ( 3) link_ALPHA1-6 : bond 0.00743 / 0.39 ( 1) link_ALPHA1-6 : angle 1.24837 / 0.98 ( 3) link_BETA1-4 : bond 0.00601 / 0.29 ( 2) link_BETA1-4 : angle 1.66739 / 1.16 ( 6) link_BETA1-6 : bond 0.00212 / 0.11 ( 1) link_BETA1-6 : angle 1.19977 / 0.91 ( 3) link_NAG-ASN : bond 0.01561 / 0.82 ( 2) link_NAG-ASN : angle 8.63287 / 5.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.157 Fit side-chains REVERT: A 378 LYS cc_start: 0.8768 (mttt) cc_final: 0.8015 (mtmt) REVERT: A 471 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8223 (mt-10) REVERT: H 43 GLN cc_start: 0.8504 (mm110) cc_final: 0.8193 (mp10) REVERT: H 70 MET cc_start: 0.9337 (mtt) cc_final: 0.8621 (mtt) REVERT: L 82 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7988 (pm20) outliers start: 8 outliers final: 6 residues processed: 38 average time/residue: 0.0543 time to fit residues: 2.9544 Evaluate side-chains 39 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.138349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.119232 restraints weight = 3931.130| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.81 r_work: 0.2767 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 3547 Z= 0.198 Angle : 0.624 15.553 4837 Z= 0.292 Chirality : 0.047 0.320 536 Planarity : 0.004 0.039 612 Dihedral : 3.990 14.549 480 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.20 % Allowed : 8.26 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.21 (0.42), residues: 427 helix: -3.83 (0.62), residues: 33 sheet: 0.29 (0.42), residues: 157 loop : 0.27 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.015 0.002 TYR A 495 PHE 0.009 0.001 PHE A 429 TRP 0.013 0.001 TRP H 47 HIS 0.005 0.002 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 ( 3534) covalent geometry : angle 0.53815 / 0.27 ( 4804) SS BOND : bond 0.00384 / 0.20 ( 6) SS BOND : angle 0.72362 / 0.41 ( 12) hydrogen bonds : bond 0.03514 / 2.17 ( 113) hydrogen bonds : angle 6.43841 / 4.50 ( 261) link_ALPHA1-3 : bond 0.00696 / 0.37 ( 1) link_ALPHA1-3 : angle 1.42582 / 1.17 ( 3) link_ALPHA1-6 : bond 0.00714 / 0.38 ( 1) link_ALPHA1-6 : angle 1.24410 / 0.96 ( 3) link_BETA1-4 : bond 0.00621 / 0.30 ( 2) link_BETA1-4 : angle 1.77516 / 1.20 ( 6) link_BETA1-6 : bond 0.00202 / 0.11 ( 1) link_BETA1-6 : angle 1.21005 / 0.89 ( 3) link_NAG-ASN : bond 0.02419 / 1.27 ( 2) link_NAG-ASN : angle 8.69029 / 6.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.127 Fit side-chains REVERT: A 378 LYS cc_start: 0.8778 (mttt) cc_final: 0.7991 (mtmt) REVERT: A 471 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8259 (mt-10) REVERT: H 43 GLN cc_start: 0.8475 (mm110) cc_final: 0.8188 (mp10) REVERT: H 70 MET cc_start: 0.9339 (mtt) cc_final: 0.8623 (mtt) REVERT: L 82 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8006 (pm20) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.0285 time to fit residues: 1.5219 Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.139311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.120348 restraints weight = 3904.533| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.80 r_work: 0.2775 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3547 Z= 0.171 Angle : 0.591 15.152 4837 Z= 0.277 Chirality : 0.045 0.258 536 Planarity : 0.004 0.037 612 Dihedral : 3.908 14.230 480 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.20 % Allowed : 8.26 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.12 (0.43), residues: 427 helix: -3.57 (0.86), residues: 21 sheet: 0.33 (0.42), residues: 157 loop : 0.40 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.012 0.001 TYR A 495 PHE 0.007 0.001 PHE L 84 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.002 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 ( 3534) covalent geometry : angle 0.51309 / 0.26 ( 4804) SS BOND : bond 0.00313 / 0.16 ( 6) SS BOND : angle 0.64950 / 0.37 ( 12) hydrogen bonds : bond 0.03348 / 2.06 ( 113) hydrogen bonds : angle 6.36268 / 4.44 ( 261) link_ALPHA1-3 : bond 0.00749 / 0.39 ( 1) link_ALPHA1-3 : angle 1.40144 / 1.15 ( 3) link_ALPHA1-6 : bond 0.00637 / 0.34 ( 1) link_ALPHA1-6 : angle 1.21316 / 0.96 ( 3) link_BETA1-4 : bond 0.00643 / 0.31 ( 2) link_BETA1-4 : angle 1.69003 / 1.15 ( 6) link_BETA1-6 : bond 0.00184 / 0.10 ( 1) link_BETA1-6 : angle 1.16312 / 0.87 ( 3) link_NAG-ASN : bond 0.02169 / 1.14 ( 2) link_NAG-ASN : angle 8.01821 / 5.52 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.080 Fit side-chains REVERT: A 378 LYS cc_start: 0.8753 (mttt) cc_final: 0.7977 (mtmt) REVERT: A 471 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8263 (mt-10) REVERT: A 506 GLN cc_start: 0.9145 (mt0) cc_final: 0.8945 (mt0) REVERT: H 43 GLN cc_start: 0.8443 (mm110) cc_final: 0.8167 (mp10) REVERT: H 70 MET cc_start: 0.9339 (mtt) cc_final: 0.8634 (mtt) REVERT: L 82 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7995 (pm20) outliers start: 8 outliers final: 7 residues processed: 37 average time/residue: 0.0314 time to fit residues: 1.6183 Evaluate side-chains 38 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.136439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.117653 restraints weight = 3910.897| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.77 r_work: 0.2750 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 3547 Z= 0.244 Angle : 0.641 14.210 4837 Z= 0.305 Chirality : 0.047 0.235 536 Planarity : 0.005 0.040 612 Dihedral : 4.175 14.940 480 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.93 % Allowed : 8.54 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.39 (0.42), residues: 427 helix: -3.85 (0.63), residues: 33 sheet: 0.23 (0.42), residues: 157 loop : 0.07 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.017 0.002 TYR A 495 PHE 0.010 0.001 PHE A 429 TRP 0.015 0.002 TRP H 47 HIS 0.006 0.002 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.24 ( 3534) covalent geometry : angle 0.57557 / 0.29 ( 4804) SS BOND : bond 0.00452 / 0.24 ( 6) SS BOND : angle 0.85017 / 0.47 ( 12) hydrogen bonds : bond 0.03762 / 2.34 ( 113) hydrogen bonds : angle 6.62099 / 4.62 ( 261) link_ALPHA1-3 : bond 0.00716 / 0.38 ( 1) link_ALPHA1-3 : angle 1.46794 / 1.19 ( 3) link_ALPHA1-6 : bond 0.00690 / 0.36 ( 1) link_ALPHA1-6 : angle 1.24586 / 0.96 ( 3) link_BETA1-4 : bond 0.00667 / 0.32 ( 2) link_BETA1-4 : angle 1.90652 / 1.24 ( 6) link_BETA1-6 : bond 0.00195 / 0.10 ( 1) link_BETA1-6 : angle 1.15072 / 0.83 ( 3) link_NAG-ASN : bond 0.01843 / 0.97 ( 2) link_NAG-ASN : angle 7.62486 / 5.13 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.078 Fit side-chains REVERT: A 378 LYS cc_start: 0.8777 (mttt) cc_final: 0.8148 (mtmt) REVERT: A 471 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8264 (mt-10) REVERT: H 70 MET cc_start: 0.9350 (mtt) cc_final: 0.8681 (mtt) outliers start: 7 outliers final: 7 residues processed: 34 average time/residue: 0.0419 time to fit residues: 2.0485 Evaluate side-chains 36 residues out of total 363 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 61 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 0 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.139384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.120710 restraints weight = 3907.641| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.78 r_work: 0.3062 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3547 Z= 0.118 Angle : 0.547 13.309 4837 Z= 0.258 Chirality : 0.044 0.221 536 Planarity : 0.004 0.035 612 Dihedral : 3.811 13.540 480 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.38 % Allowed : 9.09 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.02 (0.43), residues: 427 helix: -3.54 (0.73), residues: 27 sheet: 0.34 (0.42), residues: 158 loop : 0.37 (0.44), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 87 TYR 0.011 0.001 TYR A 369 PHE 0.007 0.001 PHE H 29 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS L 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 3534) covalent geometry : angle 0.48422 / 0.24 ( 4804) SS BOND : bond 0.00241 / 0.11 ( 6) SS BOND : angle 0.61993 / 0.35 ( 12) hydrogen bonds : bond 0.03090 / 1.89 ( 113) hydrogen bonds : angle 6.22768 / 4.33 ( 261) link_ALPHA1-3 : bond 0.00738 / 0.39 ( 1) link_ALPHA1-3 : angle 1.37101 / 1.13 ( 3) link_ALPHA1-6 : bond 0.00710 / 0.37 ( 1) link_ALPHA1-6 : angle 1.29032 / 1.04 ( 3) link_BETA1-4 : bond 0.00577 / 0.28 ( 2) link_BETA1-4 : angle 1.53231 / 1.06 ( 6) link_BETA1-6 : bond 0.00250 / 0.13 ( 1) link_BETA1-6 : angle 1.13157 / 0.87 ( 3) link_NAG-ASN : bond 0.01692 / 0.89 ( 2) link_NAG-ASN : angle 6.92362 / 4.51 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1143.56 seconds wall clock time: 20 minutes 14.62 seconds (1214.62 seconds total)