Starting phenix.real_space_refine on Wed Mar 5 19:23:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jva_22497/03_2025/7jva_22497.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jva_22497/03_2025/7jva_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_22497/03_2025/7jva_22497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jva_22497/03_2025/7jva_22497.map" model { file = "/net/cci-nas-00/data/ceres_data/7jva_22497/03_2025/7jva_22497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jva_22497/03_2025/7jva_22497.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 3, '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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.39, per 1000 atoms: 1.04 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: 0.79 Conformation dependent library (CDL) restraints added in 359.8 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: 0.43 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: 0.86 Time building geometry restraints manager: 0.94 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 - 21.24: 1898 21.24 - 42.49: 57 42.49 - 63.73: 8 63.73 - 84.98: 8 84.98 - 106.22: 5 Dihedral angle restraints: 1976 sinusoidal: 767 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=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.51 106.22 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 47.62 -57.96 105.58 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 1973 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: 5.280 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.230 Find NCS groups from input model: 0.030 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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 3332 Z= 1.020 Angle : 1.515 20.747 4539 Z= 0.982 Chirality : 0.093 0.560 496 Planarity : 0.006 0.034 585 Dihedral : 13.100 106.220 1192 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (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 TRP 0.025 0.007 TRP H 33 HIS 0.002 0.001 HIS L 8 PHE 0.024 0.004 PHE H 29 TYR 0.036 0.006 TYR H 108 ARG 0.007 0.001 ARG H 72 *********************** 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 : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 91 THR cc_start: 0.8640 (m) cc_final: 0.8342 (t) REVERT: L 37 TYR cc_start: 0.9058 (m-80) cc_final: 0.8676 (m-10) REVERT: A 375 SER cc_start: 0.8854 (m) cc_final: 0.8575 (t) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.1986 time to fit residues: 23.0894 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 : 0.328 ------------------------------------------------------------------------------- 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 34 optimal weight: 0.3980 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.0970 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.124265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.113504 restraints weight = 5670.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.116454 restraints weight = 2933.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.118415 restraints weight = 1794.971| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3332 Z= 0.241 Angle : 0.684 9.160 4539 Z= 0.360 Chirality : 0.047 0.186 496 Planarity : 0.004 0.033 585 Dihedral : 9.847 67.345 525 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 0.49 % Favored : 99.27 % Rotamer: Outliers : 2.44 % Allowed : 10.98 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.42), residues: 412 helix: -3.38 (0.71), residues: 28 sheet: 0.41 (0.41), residues: 150 loop : 1.20 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 33 HIS 0.003 0.001 HIS L 99 PHE 0.013 0.002 PHE H 106 TYR 0.022 0.002 TYR H 32 ARG 0.004 0.001 ARG L 62 *********************** 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 82 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 12 VAL cc_start: 0.6286 (OUTLIER) cc_final: 0.5987 (m) REVERT: H 91 THR cc_start: 0.8588 (m) cc_final: 0.8372 (t) REVERT: L 37 TYR cc_start: 0.9024 (m-80) cc_final: 0.8805 (m-10) REVERT: L 62 ARG cc_start: 0.8106 (ptt-90) cc_final: 0.7846 (ptt-90) REVERT: A 375 SER cc_start: 0.8931 (m) cc_final: 0.8587 (t) outliers start: 8 outliers final: 7 residues processed: 78 average time/residue: 0.1466 time to fit residues: 14.1091 Evaluate side-chains 75 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL 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 443 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN L 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.116798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.105821 restraints weight = 5722.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.108714 restraints weight = 3009.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.110609 restraints weight = 1868.652| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 3332 Z= 0.448 Angle : 0.777 11.744 4539 Z= 0.397 Chirality : 0.050 0.183 496 Planarity : 0.005 0.047 585 Dihedral : 7.252 35.268 523 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.66 % Allowed : 11.59 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.41), residues: 412 helix: -3.66 (0.63), residues: 28 sheet: 0.22 (0.43), residues: 147 loop : 0.68 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 33 HIS 0.007 0.004 HIS L 99 PHE 0.020 0.002 PHE H 68 TYR 0.021 0.002 TYR A 495 ARG 0.004 0.001 ARG H 72 *********************** 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 82 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.8009 (ptt-90) REVERT: A 441 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8343 (mp) REVERT: A 506 GLN cc_start: 0.8467 (mp10) cc_final: 0.7996 (mp10) outliers start: 12 outliers final: 5 residues processed: 77 average time/residue: 0.1554 time to fit residues: 14.6632 Evaluate side-chains 70 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 399 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** 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 = 0.3740 r_free = 0.3740 target = 0.115565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.104040 restraints weight = 5964.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.106941 restraints weight = 3207.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.108867 restraints weight = 2036.869| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 3332 Z= 0.430 Angle : 0.753 12.199 4539 Z= 0.383 Chirality : 0.050 0.178 496 Planarity : 0.005 0.060 585 Dihedral : 6.423 36.195 523 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.79 % Allowed : 12.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.41), residues: 412 helix: -3.67 (0.63), residues: 28 sheet: -0.17 (0.43), residues: 147 loop : 0.38 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 33 HIS 0.007 0.003 HIS A 519 PHE 0.013 0.002 PHE H 80 TYR 0.027 0.002 TYR H 32 ARG 0.013 0.001 ARG H 98 *********************** 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 92 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.7097 (mp0) cc_final: 0.6832 (mp0) REVERT: H 98 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8320 (ttt-90) REVERT: L 109 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8563 (p) REVERT: A 375 SER cc_start: 0.9046 (m) cc_final: 0.8663 (t) REVERT: A 506 GLN cc_start: 0.8573 (mp10) cc_final: 0.8169 (mp10) outliers start: 19 outliers final: 10 residues processed: 82 average time/residue: 0.1365 time to fit residues: 13.9495 Evaluate side-chains 83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 98 ARG 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 76 LEU 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 399 SER Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.4980 chunk 28 optimal weight: 0.0670 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 24 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.109006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.099425 restraints weight = 6019.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.101763 restraints weight = 3456.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.103363 restraints weight = 2252.827| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3332 Z= 0.268 Angle : 0.663 11.245 4539 Z= 0.335 Chirality : 0.047 0.164 496 Planarity : 0.004 0.042 585 Dihedral : 5.964 36.846 523 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.27 % Allowed : 15.24 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.41), residues: 412 helix: -2.97 (0.92), residues: 21 sheet: -0.33 (0.43), residues: 149 loop : 0.38 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 33 HIS 0.004 0.002 HIS A 519 PHE 0.013 0.002 PHE H 29 TYR 0.019 0.002 TYR H 32 ARG 0.011 0.001 ARG H 98 *********************** 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 88 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 109 THR cc_start: 0.8790 (m) cc_final: 0.8574 (p) REVERT: A 375 SER cc_start: 0.8963 (m) cc_final: 0.8607 (t) outliers start: 14 outliers final: 10 residues processed: 82 average time/residue: 0.1551 time to fit residues: 15.5540 Evaluate side-chains 78 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain L residue 52 ASP 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 91 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.109164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.099609 restraints weight = 6129.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.101856 restraints weight = 3469.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.103505 restraints weight = 2296.018| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3332 Z= 0.266 Angle : 0.697 16.168 4539 Z= 0.341 Chirality : 0.046 0.166 496 Planarity : 0.004 0.045 585 Dihedral : 5.823 36.770 523 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.96 % Allowed : 17.07 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.42), residues: 412 helix: -2.76 (0.95), residues: 21 sheet: -0.43 (0.43), residues: 149 loop : 0.40 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 109 HIS 0.006 0.002 HIS L 99 PHE 0.010 0.001 PHE H 29 TYR 0.017 0.002 TYR A 508 ARG 0.004 0.000 ARG L 62 *********************** 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 85 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 55 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7864 (ptt-90) REVERT: A 333 THR cc_start: 0.7914 (m) cc_final: 0.7696 (p) REVERT: A 375 SER cc_start: 0.8970 (m) cc_final: 0.8658 (t) outliers start: 13 outliers final: 9 residues processed: 79 average time/residue: 0.1520 time to fit residues: 14.5664 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 : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain L residue 52 ASP 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 A residue 399 SER Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.0170 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 10 optimal weight: 0.0980 chunk 36 optimal weight: 0.2980 chunk 28 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.0980 chunk 29 optimal weight: 0.3980 overall best weight: 0.1418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.111604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102011 restraints weight = 5917.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104387 restraints weight = 3376.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.106013 restraints weight = 2194.172| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 3332 Z= 0.173 Angle : 0.657 15.617 4539 Z= 0.320 Chirality : 0.044 0.147 496 Planarity : 0.004 0.040 585 Dihedral : 5.478 35.337 523 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.74 % Allowed : 18.60 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.42), residues: 412 helix: -2.69 (1.34), residues: 13 sheet: -0.34 (0.44), residues: 145 loop : 0.64 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 109 HIS 0.005 0.002 HIS L 99 PHE 0.009 0.001 PHE H 29 TYR 0.015 0.001 TYR A 508 ARG 0.008 0.001 ARG H 98 *********************** 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 84 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8236 (pp) REVERT: L 4 LEU cc_start: 0.9104 (mm) cc_final: 0.8900 (mp) REVERT: L 55 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7818 (ptt-90) REVERT: L 101 VAL cc_start: 0.9211 (t) cc_final: 0.8963 (m) REVERT: A 333 THR cc_start: 0.7883 (m) cc_final: 0.7678 (p) REVERT: A 375 SER cc_start: 0.9057 (m) cc_final: 0.8664 (t) outliers start: 9 outliers final: 4 residues processed: 80 average time/residue: 0.1468 time to fit residues: 14.3357 Evaluate side-chains 74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 76 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 23 optimal weight: 0.0970 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 1 optimal weight: 0.0000 chunk 13 optimal weight: 0.3980 chunk 40 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.3566 r_free = 0.3566 target = 0.112217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.102985 restraints weight = 5931.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.105290 restraints weight = 3432.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.106841 restraints weight = 2240.865| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 3332 Z= 0.181 Angle : 0.647 14.651 4539 Z= 0.317 Chirality : 0.044 0.146 496 Planarity : 0.004 0.062 585 Dihedral : 5.336 34.082 523 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.83 % Allowed : 18.60 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.43), residues: 412 helix: -2.99 (0.94), residues: 21 sheet: -0.13 (0.44), residues: 144 loop : 0.70 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 109 HIS 0.005 0.002 HIS L 99 PHE 0.013 0.001 PHE H 29 TYR 0.016 0.001 TYR H 32 ARG 0.007 0.001 ARG H 98 *********************** 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 80 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 11 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8212 (pp) REVERT: L 55 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7816 (ptt-90) REVERT: L 101 VAL cc_start: 0.9176 (t) cc_final: 0.8962 (m) REVERT: A 333 THR cc_start: 0.7903 (m) cc_final: 0.7702 (p) REVERT: A 375 SER cc_start: 0.8984 (m) cc_final: 0.8647 (t) outliers start: 6 outliers final: 3 residues processed: 78 average time/residue: 0.1339 time to fit residues: 13.0422 Evaluate side-chains 73 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 76 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.0060 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 11 optimal weight: 0.0870 chunk 37 optimal weight: 0.3980 overall best weight: 0.1372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.3587 r_free = 0.3587 target = 0.113410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.104165 restraints weight = 6033.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106428 restraints weight = 3484.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.107959 restraints weight = 2292.248| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 3332 Z= 0.166 Angle : 0.659 14.536 4539 Z= 0.319 Chirality : 0.044 0.168 496 Planarity : 0.004 0.048 585 Dihedral : 5.187 32.515 523 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.83 % Allowed : 19.21 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.43), residues: 412 helix: -3.10 (0.93), residues: 21 sheet: -0.09 (0.44), residues: 144 loop : 0.71 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.004 0.002 HIS L 99 PHE 0.013 0.001 PHE H 29 TYR 0.012 0.001 TYR H 59 ARG 0.009 0.001 ARG H 98 *********************** 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 74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: H 11 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8226 (pp) REVERT: A 333 THR cc_start: 0.7897 (m) cc_final: 0.7692 (p) REVERT: A 375 SER cc_start: 0.8976 (m) cc_final: 0.8657 (t) outliers start: 6 outliers final: 4 residues processed: 71 average time/residue: 0.1137 time to fit residues: 10.4628 Evaluate side-chains 70 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.0970 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 36 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 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 = 0.3552 r_free = 0.3552 target = 0.110963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101682 restraints weight = 5962.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.103917 restraints weight = 3462.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.105448 restraints weight = 2284.226| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3332 Z= 0.269 Angle : 0.703 15.040 4539 Z= 0.343 Chirality : 0.045 0.188 496 Planarity : 0.004 0.053 585 Dihedral : 5.424 33.673 523 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.83 % Allowed : 19.21 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.43), residues: 412 helix: -3.02 (0.95), residues: 21 sheet: -0.07 (0.44), residues: 148 loop : 0.68 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 101 HIS 0.004 0.002 HIS A 519 PHE 0.013 0.001 PHE H 29 TYR 0.014 0.002 TYR H 32 ARG 0.009 0.001 ARG H 98 ********************** 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 70 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: H 11 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8195 (pp) REVERT: A 333 THR cc_start: 0.7915 (m) cc_final: 0.7708 (p) REVERT: A 375 SER cc_start: 0.9009 (m) cc_final: 0.8701 (t) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.1172 time to fit residues: 10.2499 Evaluate side-chains 68 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 3 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 17 optimal weight: 0.0970 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.110213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.101025 restraints weight = 5926.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.103304 restraints weight = 3426.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.104810 restraints weight = 2236.388| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 3332 Z= 0.226 Angle : 0.683 14.864 4539 Z= 0.332 Chirality : 0.044 0.149 496 Planarity : 0.004 0.049 585 Dihedral : 5.340 34.182 523 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.52 % Allowed : 20.43 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.43), residues: 412 helix: -3.09 (0.97), residues: 21 sheet: -0.11 (0.44), residues: 141 loop : 0.59 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.004 0.002 HIS L 99 PHE 0.011 0.001 PHE H 29 TYR 0.012 0.001 TYR H 32 ARG 0.008 0.001 ARG H 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1649.24 seconds wall clock time: 29 minutes 20.60 seconds (1760.60 seconds total)