Starting phenix.real_space_refine on Wed Jul 1 22:12:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jva_22497/07_2026/7jva_22497.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jva_22497/07_2026/7jva_22497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jva_22497/07_2026/7jva_22497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jva_22497/07_2026/7jva_22497.map" model { file = "/net/cci-nas-00/data/ceres_data/7jva_22497/07_2026/7jva_22497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jva_22497/07_2026/7jva_22497.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7jva_22497/07_2026/7jva_22497.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jva_22497/07_2026/7jva_22497.cif" } resolution = 3.6 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= 0.021 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 15 5.16 5 C 2068 2.51 5 N 548 2.21 5 O 617 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: 3248 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 911 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 103} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1495 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 181} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.88, per 1000 atoms: 0.27 Number of scatterers: 3248 At special positions: 0 Unit cell: (89.25, 75.6, 70.35, 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 15 16.00 O 617 8.00 N 548 7.00 C 2068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.09 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 118.1 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 10 sheets defined 13.3% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... 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 Processing helix chain 'L' and resid 28 through 32 removed outlier: 4.028A pdb=" N ASN L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 71 No H-bonds generated for 'chain 'L' and resid 69 through 71' Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.358A 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 sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.815A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.922A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 5.951A pdb=" N GLN L 38 " --> pdb=" O THR L 47 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N THR L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.530A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 129 hydrogen bonds defined for protein. 285 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: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 586 1.31 - 1.45: 1042 1.45 - 1.58: 1682 1.58 - 1.71: 4 1.71 - 1.84: 18 Bond restraints: 3332 Sorted by residual: bond pdb=" CD GLU H 6 " pdb=" OE2 GLU H 6 " ideal model delta sigma weight residual 1.249 1.182 0.067 1.90e-02 2.77e+03 1.23e+01 bond pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 9.92e+00 bond pdb=" CB ASN H 50 " pdb=" CG ASN H 50 " ideal model delta sigma weight residual 1.516 1.437 0.079 2.50e-02 1.60e+03 9.89e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.476 -0.063 2.00e-02 2.50e+03 9.85e+00 bond pdb=" NE ARG A 357 " pdb=" CZ ARG A 357 " ideal model delta sigma weight residual 1.326 1.360 -0.034 1.10e-02 8.26e+03 9.59e+00 ... (remaining 3327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.15: 4438 4.15 - 8.30: 98 8.30 - 12.45: 1 12.45 - 16.60: 0 16.60 - 20.75: 2 Bond angle restraints: 4539 Sorted by residual: angle pdb=" CD1 LEU H 86 " pdb=" CG LEU H 86 " pdb=" CD2 LEU H 86 " ideal model delta sigma weight residual 110.80 131.55 -20.75 2.20e+00 2.07e-01 8.89e+01 angle pdb=" CG1 VAL H 2 " pdb=" CB VAL H 2 " pdb=" CG2 VAL H 2 " ideal model delta sigma weight residual 110.80 131.11 -20.31 2.20e+00 2.07e-01 8.52e+01 angle pdb=" C SER A 383 " pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta sigma weight residual 119.56 127.19 -7.63 1.02e+00 9.61e-01 5.60e+01 angle pdb=" C LEU A 425 " pdb=" N PRO A 426 " pdb=" CA PRO A 426 " ideal model delta sigma weight residual 119.85 126.34 -6.49 1.01e+00 9.80e-01 4.12e+01 angle pdb=" C GLN A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.56 126.05 -6.49 1.02e+00 9.61e-01 4.04e+01 ... (remaining 4534 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 1823 16.77 - 33.53: 74 33.53 - 50.30: 11 50.30 - 67.06: 6 67.06 - 83.83: 1 Dihedral angle restraints: 1915 sinusoidal: 706 harmonic: 1209 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -36.13 -49.87 1 1.00e+01 1.00e-02 3.41e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 91 " pdb=" CB CYS L 91 " ideal model delta sinusoidal sigma weight residual 93.00 67.40 25.60 1 1.00e+01 1.00e-02 9.42e+00 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 93.00 118.10 -25.10 1 1.00e+01 1.00e-02 9.07e+00 ... (remaining 1912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 422 0.112 - 0.224: 60 0.224 - 0.336: 9 0.336 - 0.448: 3 0.448 - 0.560: 2 Chirality restraints: 496 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 -2.62 0.22 2.00e-02 2.50e+03 1.25e+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 -2.48 0.08 2.00e-02 2.50e+03 1.68e+01 chirality pdb=" CG LEU H 86 " pdb=" CB LEU H 86 " pdb=" CD1 LEU H 86 " pdb=" CD2 LEU H 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.83e+00 ... (remaining 493 not shown) Planarity restraints: 586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 108 " 0.036 2.00e-02 2.50e+03 1.86e-02 6.92e+00 pdb=" CG TYR H 108 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR H 108 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR H 108 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR H 108 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR H 108 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR H 108 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 108 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 495 " -0.035 2.00e-02 2.50e+03 1.83e-02 6.70e+00 pdb=" CG TYR A 495 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 495 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 495 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 495 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 495 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 495 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 495 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 37 " 0.027 2.00e-02 2.50e+03 1.51e-02 4.59e+00 pdb=" CG TYR L 37 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR L 37 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR L 37 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR L 37 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR L 37 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR L 37 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 37 " 0.024 2.00e-02 2.50e+03 ... (remaining 583 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1320 2.90 - 3.40: 2801 3.40 - 3.90: 5451 3.90 - 4.40: 6366 4.40 - 4.90: 10508 Nonbonded interactions: 26446 Sorted by model distance: nonbonded pdb=" OD2 ASP L 52 " pdb=" NZ LYS A 378 " model vdw 2.398 3.120 nonbonded pdb=" OE2 GLU H 6 " pdb=" N GLN H 111 " model vdw 2.536 3.120 nonbonded pdb=" N ASN A 440 " pdb=" OD1 ASN A 440 " model vdw 2.551 3.120 nonbonded pdb=" N ASP A 428 " pdb=" OD1 ASP A 428 " model vdw 2.552 3.120 nonbonded pdb=" N CYS H 96 " pdb=" O CYS H 96 " model vdw 2.557 2.496 ... (remaining 26441 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 group one per residue 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: 4.650 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.800 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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: 10.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.016 0.079 3341 Z= 0.861 Angle : 1.533 20.747 4560 Z= 0.985 Chirality : 0.093 0.560 496 Planarity : 0.006 0.034 585 Dihedral : 10.088 83.827 1131 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 0.80 Ramachandran Plot: Outliers : 0.24 % Allowed : 0.97 % Favored : 98.79 % Rotamer: Outliers : 0.30 % Allowed : 1.22 % Favored : 98.48 % 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: 0.87 (0.43), residues: 412 helix: -4.22 (0.39), residues: 28 sheet: 0.47 (0.42), residues: 154 loop : 1.57 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 72 TYR 0.036 0.006 TYR H 108 PHE 0.024 0.004 PHE H 29 TRP 0.025 0.007 TRP H 33 HIS 0.002 0.001 HIS L 8 Details of bonding type rmsd/Z covalent geometry : bond 0.01578 / 0.85 ( 3332) covalent geometry : angle 1.51478 / 0.98 ( 4539) SS BOND : bond 0.02855 / 1.41 ( 6) SS BOND : angle 3.67329 / 2.01 ( 12) hydrogen bonds : bond 0.19354 / 13.64 ( 117) hydrogen bonds : angle 8.62319 / 5.99 ( 285) link_BETA1-4 : bond 0.07331 / 3.70 ( 2) link_BETA1-4 : angle 4.68704 / 2.67 ( 6) link_NAG-ASN : bond 0.05556 / 2.92 ( 1) link_NAG-ASN : angle 2.05395 / 1.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 91 THR cc_start: 0.8641 (m) cc_final: 0.8333 (t) REVERT: L 37 TYR cc_start: 0.9058 (m-80) cc_final: 0.8693 (m-10) REVERT: A 375 SER cc_start: 0.8854 (m) cc_final: 0.8574 (t) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.0821 time to fit residues: 9.6036 Evaluate side-chains 64 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 38 GLN L 99 HIS A 394 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.122638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.111900 restraints weight = 5823.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.114888 restraints weight = 2998.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116830 restraints weight = 1829.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.118116 restraints weight = 1243.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.119033 restraints weight = 906.250| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3341 Z= 0.214 Angle : 0.738 9.064 4560 Z= 0.378 Chirality : 0.048 0.158 496 Planarity : 0.005 0.034 585 Dihedral : 5.213 26.087 464 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 0.73 % Favored : 99.03 % Rotamer: Outliers : 2.74 % Allowed : 10.98 % Favored : 86.28 % 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: 0.61 (0.42), residues: 412 helix: -3.53 (0.64), residues: 28 sheet: 0.40 (0.41), residues: 150 loop : 1.15 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 62 TYR 0.021 0.002 TYR H 32 PHE 0.015 0.002 PHE A 456 TRP 0.020 0.002 TRP H 33 HIS 0.003 0.002 HIS L 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 ( 3332) covalent geometry : angle 0.71075 / 0.37 ( 4539) SS BOND : bond 0.00386 / 0.20 ( 6) SS BOND : angle 1.76136 / 0.97 ( 12) hydrogen bonds : bond 0.04593 / 3.22 ( 117) hydrogen bonds : angle 6.91823 / 4.69 ( 285) link_BETA1-4 : bond 0.00622 / 0.32 ( 2) link_BETA1-4 : angle 4.16442 / 2.16 ( 6) link_NAG-ASN : bond 0.00077 / 0.04 ( 1) link_NAG-ASN : angle 4.07859 / 2.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.9045 (m-80) cc_final: 0.8842 (m-80) REVERT: H 91 THR cc_start: 0.8609 (m) cc_final: 0.8393 (t) REVERT: L 37 TYR cc_start: 0.9013 (m-80) cc_final: 0.8772 (m-10) REVERT: A 375 SER cc_start: 0.8907 (m) cc_final: 0.8552 (t) REVERT: A 441 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8266 (mp) outliers start: 9 outliers final: 7 residues processed: 81 average time/residue: 0.0658 time to fit residues: 6.5716 Evaluate side-chains 72 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 443 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 0.0570 chunk 1 optimal weight: 0.0370 chunk 29 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.122465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.111686 restraints weight = 5683.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.114653 restraints weight = 2929.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.116601 restraints weight = 1786.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.117946 restraints weight = 1206.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.118758 restraints weight = 868.985| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 3341 Z= 0.150 Angle : 0.666 10.833 4560 Z= 0.333 Chirality : 0.045 0.143 496 Planarity : 0.004 0.037 585 Dihedral : 5.002 24.151 462 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 4.57 % Allowed : 10.37 % Favored : 85.06 % 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: 0.53 (0.42), residues: 412 helix: -3.33 (0.72), residues: 28 sheet: 0.35 (0.42), residues: 149 loop : 1.05 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 98 TYR 0.013 0.001 TYR H 32 PHE 0.011 0.001 PHE H 106 TRP 0.016 0.001 TRP H 33 HIS 0.004 0.001 HIS L 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 3332) covalent geometry : angle 0.65042 / 0.33 ( 4539) SS BOND : bond 0.00352 / 0.21 ( 6) SS BOND : angle 1.22981 / 0.61 ( 12) hydrogen bonds : bond 0.04084 / 2.90 ( 117) hydrogen bonds : angle 6.60421 / 4.45 ( 285) link_BETA1-4 : bond 0.00817 / 0.42 ( 2) link_BETA1-4 : angle 3.37204 / 1.77 ( 6) link_NAG-ASN : bond 0.00548 / 0.29 ( 1) link_NAG-ASN : angle 2.22475 / 1.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7887 (ptt-90) REVERT: A 375 SER cc_start: 0.8930 (m) cc_final: 0.8602 (t) REVERT: A 441 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8278 (mp) REVERT: A 506 GLN cc_start: 0.8245 (mp10) cc_final: 0.7871 (mp10) outliers start: 15 outliers final: 8 residues processed: 80 average time/residue: 0.0578 time to fit residues: 5.8066 Evaluate side-chains 73 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 443 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.0770 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.0050 overall best weight: 0.3952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.120413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.109272 restraints weight = 5757.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.112243 restraints weight = 3037.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.114166 restraints weight = 1876.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.115472 restraints weight = 1292.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.116425 restraints weight = 947.383| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3341 Z= 0.188 Angle : 0.676 10.414 4560 Z= 0.337 Chirality : 0.046 0.154 496 Planarity : 0.005 0.054 585 Dihedral : 5.013 25.030 462 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 4.57 % Allowed : 11.59 % Favored : 83.84 % 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: 0.40 (0.42), residues: 412 helix: -2.85 (0.95), residues: 21 sheet: 0.20 (0.43), residues: 149 loop : 0.80 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 62 TYR 0.013 0.001 TYR A 495 PHE 0.009 0.002 PHE H 106 TRP 0.011 0.001 TRP H 33 HIS 0.003 0.002 HIS L 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 3332) covalent geometry : angle 0.66160 / 0.33 ( 4539) SS BOND : bond 0.00285 / 0.13 ( 6) SS BOND : angle 1.47065 / 0.78 ( 12) hydrogen bonds : bond 0.03976 / 2.86 ( 117) hydrogen bonds : angle 6.37453 / 4.29 ( 285) link_BETA1-4 : bond 0.00830 / 0.42 ( 2) link_BETA1-4 : angle 3.13499 / 1.65 ( 6) link_NAG-ASN : bond 0.00527 / 0.28 ( 1) link_NAG-ASN : angle 1.81358 / 0.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6495 (t70) REVERT: L 55 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7912 (ptt-90) REVERT: L 67 ILE cc_start: 0.8580 (mt) cc_final: 0.8328 (mt) REVERT: L 109 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8413 (p) REVERT: A 375 SER cc_start: 0.8933 (m) cc_final: 0.8611 (t) REVERT: A 441 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8326 (mp) REVERT: A 506 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7987 (mp10) outliers start: 15 outliers final: 8 residues processed: 77 average time/residue: 0.0599 time to fit residues: 5.7516 Evaluate side-chains 79 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 91 CYS Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 506 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.6980 chunk 16 optimal weight: 0.0670 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.0770 chunk 38 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 0.4980 chunk 40 optimal weight: 0.3980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.121091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.110055 restraints weight = 5738.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.112958 restraints weight = 2998.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.114865 restraints weight = 1873.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.116125 restraints weight = 1291.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.117069 restraints weight = 957.656| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3341 Z= 0.149 Angle : 0.643 10.448 4560 Z= 0.320 Chirality : 0.045 0.146 496 Planarity : 0.004 0.052 585 Dihedral : 4.854 24.604 462 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.88 % Allowed : 11.28 % Favored : 83.84 % 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: 0.42 (0.42), residues: 412 helix: -2.66 (1.01), residues: 21 sheet: 0.10 (0.42), residues: 151 loop : 0.88 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 62 TYR 0.012 0.001 TYR A 369 PHE 0.012 0.001 PHE A 456 TRP 0.009 0.001 TRP H 33 HIS 0.003 0.002 HIS L 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 3332) covalent geometry : angle 0.63174 / 0.32 ( 4539) SS BOND : bond 0.00383 / 0.24 ( 6) SS BOND : angle 1.19950 / 0.62 ( 12) hydrogen bonds : bond 0.03676 / 2.65 ( 117) hydrogen bonds : angle 6.25290 / 4.19 ( 285) link_BETA1-4 : bond 0.00896 / 0.45 ( 2) link_BETA1-4 : angle 2.95387 / 1.54 ( 6) link_NAG-ASN : bond 0.00501 / 0.26 ( 1) link_NAG-ASN : angle 1.48361 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7870 (ptt-90) REVERT: L 109 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8482 (p) REVERT: A 441 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8348 (mp) REVERT: A 506 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8068 (mp10) outliers start: 16 outliers final: 5 residues processed: 83 average time/residue: 0.0664 time to fit residues: 6.7200 Evaluate side-chains 77 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 506 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 0.0270 chunk 21 optimal weight: 0.4980 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.117166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.105630 restraints weight = 5917.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.108629 restraints weight = 3131.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.110599 restraints weight = 1950.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.111913 restraints weight = 1355.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.112794 restraints weight = 1007.150| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3341 Z= 0.173 Angle : 0.664 10.472 4560 Z= 0.331 Chirality : 0.045 0.152 496 Planarity : 0.004 0.039 585 Dihedral : 4.794 24.609 462 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.96 % Allowed : 12.50 % Favored : 83.54 % 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: 0.31 (0.42), residues: 412 helix: -2.64 (1.00), residues: 21 sheet: -0.02 (0.42), residues: 151 loop : 0.84 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 98 TYR 0.012 0.001 TYR A 495 PHE 0.013 0.001 PHE A 456 TRP 0.009 0.001 TRP H 33 HIS 0.003 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 3332) covalent geometry : angle 0.65295 / 0.33 ( 4539) SS BOND : bond 0.00306 / 0.16 ( 6) SS BOND : angle 1.31727 / 0.67 ( 12) hydrogen bonds : bond 0.03675 / 2.63 ( 117) hydrogen bonds : angle 6.17448 / 4.13 ( 285) link_BETA1-4 : bond 0.00900 / 0.46 ( 2) link_BETA1-4 : angle 2.81988 / 1.47 ( 6) link_NAG-ASN : bond 0.00499 / 0.26 ( 1) link_NAG-ASN : angle 1.50323 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6858 (mp0) cc_final: 0.6445 (mp0) REVERT: L 55 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8017 (ptt-90) REVERT: L 109 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8553 (p) REVERT: A 506 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8090 (mp10) outliers start: 13 outliers final: 7 residues processed: 77 average time/residue: 0.0622 time to fit residues: 5.9155 Evaluate side-chains 76 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 86 GLU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 506 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.3980 chunk 26 optimal weight: 0.2980 chunk 6 optimal weight: 0.0770 chunk 5 optimal weight: 0.3980 chunk 36 optimal weight: 0.0980 overall best weight: 0.2338 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.121655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.110198 restraints weight = 5863.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.113184 restraints weight = 3119.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.115119 restraints weight = 1945.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.116447 restraints weight = 1351.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.117314 restraints weight = 1001.572| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3341 Z= 0.134 Angle : 0.628 10.349 4560 Z= 0.312 Chirality : 0.044 0.143 496 Planarity : 0.004 0.041 585 Dihedral : 4.571 23.165 462 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.05 % Allowed : 14.33 % Favored : 82.62 % 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: 0.37 (0.42), residues: 412 helix: -2.45 (1.06), residues: 21 sheet: -0.03 (0.43), residues: 147 loop : 0.89 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 62 TYR 0.011 0.001 TYR A 369 PHE 0.010 0.001 PHE A 456 TRP 0.008 0.001 TRP H 33 HIS 0.003 0.001 HIS L 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 3332) covalent geometry : angle 0.61683 / 0.31 ( 4539) SS BOND : bond 0.00264 / 0.16 ( 6) SS BOND : angle 1.29506 / 0.65 ( 12) hydrogen bonds : bond 0.03407 / 2.40 ( 117) hydrogen bonds : angle 6.10698 / 4.07 ( 285) link_BETA1-4 : bond 0.00800 / 0.41 ( 2) link_BETA1-4 : angle 2.66996 / 1.38 ( 6) link_NAG-ASN : bond 0.00440 / 0.23 ( 1) link_NAG-ASN : angle 1.39070 / 0.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.8034 (ptt-90) REVERT: L 101 VAL cc_start: 0.9279 (t) cc_final: 0.9038 (m) REVERT: A 506 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.8129 (mp10) outliers start: 10 outliers final: 5 residues processed: 79 average time/residue: 0.0549 time to fit residues: 5.4990 Evaluate side-chains 74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 506 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 0.0870 chunk 17 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.0270 chunk 8 optimal weight: 0.4980 overall best weight: 0.3216 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.111740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102126 restraints weight = 5967.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.104550 restraints weight = 3383.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.106134 restraints weight = 2182.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.107255 restraints weight = 1536.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.107939 restraints weight = 1145.624| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3341 Z= 0.162 Angle : 0.653 10.051 4560 Z= 0.322 Chirality : 0.045 0.153 496 Planarity : 0.004 0.040 585 Dihedral : 4.567 23.569 462 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.44 % Allowed : 15.55 % Favored : 82.01 % 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: 0.25 (0.43), residues: 412 helix: -2.22 (1.14), residues: 21 sheet: -0.17 (0.43), residues: 151 loop : 0.83 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 62 TYR 0.018 0.001 TYR A 508 PHE 0.014 0.001 PHE A 456 TRP 0.006 0.001 TRP H 33 HIS 0.003 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 3332) covalent geometry : angle 0.64277 / 0.32 ( 4539) SS BOND : bond 0.00252 / 0.12 ( 6) SS BOND : angle 1.31353 / 0.67 ( 12) hydrogen bonds : bond 0.03391 / 2.41 ( 117) hydrogen bonds : angle 6.12970 / 4.08 ( 285) link_BETA1-4 : bond 0.00850 / 0.43 ( 2) link_BETA1-4 : angle 2.60397 / 1.34 ( 6) link_NAG-ASN : bond 0.00433 / 0.23 ( 1) link_NAG-ASN : angle 1.51028 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 99 VAL cc_start: 0.9097 (t) cc_final: 0.8896 (p) REVERT: L 101 VAL cc_start: 0.9243 (t) cc_final: 0.9010 (m) REVERT: A 333 THR cc_start: 0.7890 (m) cc_final: 0.7675 (p) outliers start: 8 outliers final: 6 residues processed: 82 average time/residue: 0.0576 time to fit residues: 5.9798 Evaluate side-chains 80 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.110818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.101465 restraints weight = 6026.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103765 restraints weight = 3453.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.105297 restraints weight = 2242.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106262 restraints weight = 1594.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.107035 restraints weight = 1211.985| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3341 Z= 0.165 Angle : 0.689 15.051 4560 Z= 0.335 Chirality : 0.045 0.150 496 Planarity : 0.004 0.038 585 Dihedral : 4.543 23.578 462 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.13 % Allowed : 16.46 % Favored : 81.40 % 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: 0.20 (0.42), residues: 412 helix: -2.63 (1.04), residues: 21 sheet: -0.14 (0.44), residues: 141 loop : 0.74 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 62 TYR 0.011 0.001 TYR A 369 PHE 0.014 0.001 PHE A 456 TRP 0.009 0.001 TRP H 33 HIS 0.003 0.002 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 3332) covalent geometry : angle 0.67977 / 0.33 ( 4539) SS BOND : bond 0.00249 / 0.13 ( 6) SS BOND : angle 1.31688 / 0.64 ( 12) hydrogen bonds : bond 0.03448 / 2.45 ( 117) hydrogen bonds : angle 6.17341 / 4.12 ( 285) link_BETA1-4 : bond 0.00882 / 0.45 ( 2) link_BETA1-4 : angle 2.55144 / 1.30 ( 6) link_NAG-ASN : bond 0.00403 / 0.21 ( 1) link_NAG-ASN : angle 1.44239 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 101 VAL cc_start: 0.9219 (t) cc_final: 0.9003 (m) REVERT: A 333 THR cc_start: 0.7901 (m) cc_final: 0.7689 (p) outliers start: 7 outliers final: 7 residues processed: 74 average time/residue: 0.0542 time to fit residues: 5.1490 Evaluate side-chains 74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.2980 chunk 16 optimal weight: 0.0670 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 28 optimal weight: 0.0870 chunk 23 optimal weight: 0.2980 overall best weight: 0.1654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 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 = 0.3585 r_free = 0.3585 target = 0.113482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.104111 restraints weight = 5975.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.106547 restraints weight = 3337.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.108180 restraints weight = 2127.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.109237 restraints weight = 1468.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.109956 restraints weight = 1092.841| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 3341 Z= 0.129 Angle : 0.687 18.311 4560 Z= 0.325 Chirality : 0.044 0.139 496 Planarity : 0.004 0.039 585 Dihedral : 4.383 22.023 462 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.83 % Allowed : 16.16 % Favored : 82.01 % 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: 0.23 (0.42), residues: 412 helix: -2.64 (1.02), residues: 21 sheet: -0.01 (0.44), residues: 138 loop : 0.68 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 62 TYR 0.009 0.001 TYR A 369 PHE 0.009 0.001 PHE A 456 TRP 0.008 0.001 TRP H 33 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.13 ( 3332) covalent geometry : angle 0.67874 / 0.32 ( 4539) SS BOND : bond 0.00239 / 0.12 ( 6) SS BOND : angle 1.18009 / 0.56 ( 12) hydrogen bonds : bond 0.03239 / 2.26 ( 117) hydrogen bonds : angle 6.00019 / 4.02 ( 285) link_BETA1-4 : bond 0.00786 / 0.40 ( 2) link_BETA1-4 : angle 2.49165 / 1.27 ( 6) link_NAG-ASN : bond 0.00363 / 0.19 ( 1) link_NAG-ASN : angle 1.30643 / 0.70 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7946 (ptt-90) REVERT: L 62 ARG cc_start: 0.7533 (ptt-90) cc_final: 0.7066 (ptt-90) REVERT: L 82 LYS cc_start: 0.7627 (mtpt) cc_final: 0.7356 (mtpt) REVERT: A 333 THR cc_start: 0.7894 (m) cc_final: 0.7684 (p) outliers start: 6 outliers final: 5 residues processed: 70 average time/residue: 0.0452 time to fit residues: 4.0743 Evaluate side-chains 70 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 0.0020 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.0070 chunk 5 optimal weight: 0.0470 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 overall best weight: 0.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.115564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.106157 restraints weight = 5935.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108530 restraints weight = 3334.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.110154 restraints weight = 2135.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.111238 restraints weight = 1486.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.111981 restraints weight = 1111.972| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 3341 Z= 0.122 Angle : 0.677 17.261 4560 Z= 0.323 Chirality : 0.043 0.135 496 Planarity : 0.004 0.038 585 Dihedral : 4.281 22.723 462 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.52 % Allowed : 16.77 % Favored : 81.71 % 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: 0.33 (0.42), residues: 412 helix: -2.91 (0.99), residues: 21 sheet: 0.15 (0.44), residues: 138 loop : 0.71 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 62 TYR 0.008 0.001 TYR A 369 PHE 0.008 0.001 PHE H 29 TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.12 ( 3332) covalent geometry : angle 0.66961 / 0.32 ( 4539) SS BOND : bond 0.00255 / 0.13 ( 6) SS BOND : angle 1.11421 / 0.52 ( 12) hydrogen bonds : bond 0.03128 / 2.16 ( 117) hydrogen bonds : angle 5.86831 / 3.92 ( 285) link_BETA1-4 : bond 0.00751 / 0.38 ( 2) link_BETA1-4 : angle 2.48914 / 1.26 ( 6) link_NAG-ASN : bond 0.00349 / 0.18 ( 1) link_NAG-ASN : angle 1.18342 / 0.64 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 925.21 seconds wall clock time: 16 minutes 35.48 seconds (995.48 seconds total)