Starting phenix.real_space_refine on Wed Jul 1 21:59:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8erq_28558/07_2026/8erq_28558.cif Found real_map, /net/cci-nas-00/data/ceres_data/8erq_28558/07_2026/8erq_28558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8erq_28558/07_2026/8erq_28558.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8erq_28558/07_2026/8erq_28558.cif" model { file = "/net/cci-nas-00/data/ceres_data/8erq_28558/07_2026/8erq_28558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8erq_28558/07_2026/8erq_28558.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8erq_28558/07_2026/8erq_28558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8erq_28558/07_2026/8erq_28558.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.049 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 2040 2.51 5 N 534 2.21 5 O 589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 3178 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 866 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 110} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 778 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1520 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 12, 'TRANS': 184} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 3, 'PHE:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 0.85, per 1000 atoms: 0.27 Number of scatterers: 3178 At special positions: 0 Unit cell: (86, 62, 96, 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 589 8.00 N 534 7.00 C 2040 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 97 " distance=2.07 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 91 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.21 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.12 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 NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 124.8 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 9.2% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'L' and resid 82 through 86 removed outlier: 4.054A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.742A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.897A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 370' Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.648A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 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 11 through 12 removed outlier: 6.704A pdb=" N VAL H 36 " --> pdb=" O LEU H 52 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU H 52 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP H 38 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.583A pdb=" N VAL L 11 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN L 40 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU L 49 " --> pdb=" O GLN L 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.583A pdb=" N VAL L 11 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.848A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.736A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) 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 474 110 hydrogen bonds defined for protein. 258 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: 0.34 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 909 1.33 - 1.46: 947 1.46 - 1.59: 1387 1.59 - 1.73: 0 1.73 - 1.86: 18 Bond restraints: 3261 Sorted by residual: bond pdb=" CB ILE H 2 " pdb=" CG1 ILE H 2 " ideal model delta sigma weight residual 1.530 1.588 -0.058 2.00e-02 2.50e+03 8.42e+00 bond pdb=" NE ARG L 64 " pdb=" CZ ARG L 64 " ideal model delta sigma weight residual 1.326 1.357 -0.031 1.10e-02 8.26e+03 7.93e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.465 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" CD GLU H 6 " pdb=" OE1 GLU H 6 " ideal model delta sigma weight residual 1.249 1.200 0.049 1.90e-02 2.77e+03 6.60e+00 bond pdb=" CG ASP L 88 " pdb=" OD1 ASP L 88 " ideal model delta sigma weight residual 1.249 1.201 0.048 1.90e-02 2.77e+03 6.39e+00 ... (remaining 3256 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 4387 3.99 - 7.97: 65 7.97 - 11.96: 2 11.96 - 15.95: 0 15.95 - 19.94: 2 Bond angle restraints: 4456 Sorted by residual: angle pdb=" CG1 VAL A 503 " pdb=" CB VAL A 503 " pdb=" CG2 VAL A 503 " ideal model delta sigma weight residual 110.80 130.74 -19.94 2.20e+00 2.07e-01 8.21e+01 angle pdb=" C ARG A 498 " pdb=" N PRO A 499 " pdb=" CA PRO A 499 " ideal model delta sigma weight residual 119.56 127.58 -8.02 1.02e+00 9.61e-01 6.19e+01 angle pdb=" C GLN H 41 " pdb=" N PRO H 42 " pdb=" CA PRO H 42 " ideal model delta sigma weight residual 119.66 124.99 -5.33 7.20e-01 1.93e+00 5.48e+01 angle pdb=" C SER A 383 " pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta sigma weight residual 119.56 126.75 -7.19 1.02e+00 9.61e-01 4.97e+01 angle pdb=" C ARG L 57 " pdb=" N PRO L 58 " pdb=" CA PRO L 58 " ideal model delta sigma weight residual 120.03 126.67 -6.64 9.90e-01 1.02e+00 4.50e+01 ... (remaining 4451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.37: 1799 15.37 - 30.75: 76 30.75 - 46.12: 26 46.12 - 61.50: 8 61.50 - 76.87: 1 Dihedral angle restraints: 1910 sinusoidal: 680 harmonic: 1230 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -40.27 -45.73 1 1.00e+01 1.00e-02 2.90e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 50.76 42.24 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CA ALA A 372 " pdb=" C ALA A 372 " pdb=" N PRO A 373 " pdb=" CA PRO A 373 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 1907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 458 0.109 - 0.218: 42 0.218 - 0.327: 1 0.327 - 0.436: 0 0.436 - 0.546: 2 Chirality restraints: 503 Sorted by residual: chirality pdb=" CG LEU A 368 " pdb=" CB LEU A 368 " pdb=" CD1 LEU A 368 " pdb=" CD2 LEU A 368 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.44e+00 chirality pdb=" CB VAL A 503 " pdb=" CA VAL A 503 " pdb=" CG1 VAL A 503 " pdb=" CG2 VAL A 503 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.82e+00 chirality pdb=" C2 NAG A1301 " pdb=" C1 NAG A1301 " pdb=" C3 NAG A1301 " pdb=" N2 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.82 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 500 not shown) Planarity restraints: 571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 516 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C GLU A 516 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU A 516 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 517 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 366 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C SER A 366 " 0.036 2.00e-02 2.50e+03 pdb=" O SER A 366 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 367 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 371 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C LEU A 371 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 371 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A 372 " 0.011 2.00e-02 2.50e+03 ... (remaining 568 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 768 2.79 - 3.32: 2533 3.32 - 3.85: 5041 3.85 - 4.37: 5896 4.37 - 4.90: 10338 Nonbonded interactions: 24576 Sorted by model distance: nonbonded pdb=" CD1 PHE A 392 " pdb=" CD2 LEU A 517 " model vdw 2.265 3.760 nonbonded pdb=" OD2 ASP H 58 " pdb=" NZ LYS A 444 " model vdw 2.385 3.120 nonbonded pdb=" OG1 THR H 21 " pdb=" NE2 GLN H 79 " model vdw 2.532 3.120 nonbonded pdb=" N ASP A 389 " pdb=" N LEU A 390 " model vdw 2.587 2.560 nonbonded pdb=" O SER A 496 " pdb=" OG SER A 496 " model vdw 2.590 3.040 ... (remaining 24571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 4.090 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.020 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.176 3268 Z= 0.606 Angle : 1.340 19.937 4471 Z= 0.878 Chirality : 0.072 0.546 503 Planarity : 0.005 0.024 570 Dihedral : 10.072 76.869 1110 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.95 % Allowed : 1.90 % Favored : 97.15 % 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: 0.38 (0.42), residues: 417 helix: -4.49 (0.46), residues: 26 sheet: 1.12 (0.43), residues: 146 loop : 0.36 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 493 TYR 0.021 0.004 TYR L 33 PHE 0.021 0.003 PHE A 374 TRP 0.017 0.004 TRP H 109 HIS 0.001 0.000 HIS L 42 Details of bonding type rmsd/Z covalent geometry : bond 0.01044 / 0.58 ( 3261) covalent geometry : angle 1.32032 / 0.87 ( 4456) SS BOND : bond 0.08242 / 3.35 ( 6) SS BOND : angle 4.59009 / 2.42 ( 12) hydrogen bonds : bond 0.17333 / 12.51 ( 103) hydrogen bonds : angle 8.37495 / 5.33 ( 258) link_NAG-ASN : bond 0.05422 / 2.85 ( 1) link_NAG-ASN : angle 2.08408 / 1.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.075 Fit side-chains REVERT: H 17 THR cc_start: 0.6167 (m) cc_final: 0.5903 (p) outliers start: 3 outliers final: 0 residues processed: 75 average time/residue: 0.0550 time to fit residues: 4.9530 Evaluate side-chains 49 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.0050 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN L 40 GLN L 41 HIS L 42 HIS A 388 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.177179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.153833 restraints weight = 3866.004| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.79 r_work: 0.3473 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3268 Z= 0.140 Angle : 0.618 11.439 4471 Z= 0.313 Chirality : 0.046 0.167 503 Planarity : 0.005 0.046 570 Dihedral : 4.390 18.107 465 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.06 % Allowed : 8.23 % Favored : 86.71 % 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: 0.49 (0.43), residues: 417 helix: -3.94 (0.78), residues: 26 sheet: 1.41 (0.44), residues: 144 loop : 0.22 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.011 0.001 TYR L 39 PHE 0.013 0.002 PHE H 24 TRP 0.011 0.001 TRP A 436 HIS 0.002 0.001 HIS H 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 3261) covalent geometry : angle 0.61731 / 0.31 ( 4456) SS BOND : bond 0.00179 / 0.08 ( 6) SS BOND : angle 0.69453 / 0.38 ( 12) hydrogen bonds : bond 0.03662 / 2.64 ( 103) hydrogen bonds : angle 6.24259 / 4.08 ( 258) link_NAG-ASN : bond 0.00350 / 0.18 ( 1) link_NAG-ASN : angle 0.93388 / 0.47 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.073 Fit side-chains REVERT: H 17 THR cc_start: 0.6314 (m) cc_final: 0.5962 (p) REVERT: A 469 SER cc_start: 0.8996 (m) cc_final: 0.8554 (p) outliers start: 16 outliers final: 9 residues processed: 64 average time/residue: 0.0566 time to fit residues: 4.4701 Evaluate side-chains 61 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 30 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.162517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.138011 restraints weight = 3766.847| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.89 r_work: 0.3402 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3268 Z= 0.188 Angle : 0.669 10.185 4471 Z= 0.339 Chirality : 0.047 0.147 503 Planarity : 0.005 0.046 570 Dihedral : 4.703 20.670 465 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.43 % Allowed : 9.81 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.06 (0.42), residues: 417 helix: -3.98 (0.77), residues: 20 sheet: 1.04 (0.43), residues: 154 loop : -0.22 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 357 TYR 0.017 0.002 TYR L 89 PHE 0.020 0.002 PHE A 377 TRP 0.011 0.002 TRP A 436 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 ( 3261) covalent geometry : angle 0.66855 / 0.34 ( 4456) SS BOND : bond 0.00203 / 0.12 ( 6) SS BOND : angle 0.69365 / 0.39 ( 12) hydrogen bonds : bond 0.04621 / 3.40 ( 103) hydrogen bonds : angle 6.05764 / 3.99 ( 258) link_NAG-ASN : bond 0.00248 / 0.13 ( 1) link_NAG-ASN : angle 1.00723 / 0.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.085 Fit side-chains REVERT: H 17 THR cc_start: 0.6789 (m) cc_final: 0.6495 (p) REVERT: H 54 TYR cc_start: 0.9045 (m-80) cc_final: 0.8770 (m-80) REVERT: L 108 THR cc_start: 0.7842 (t) cc_final: 0.7599 (p) REVERT: A 468 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.7826 (pt) outliers start: 14 outliers final: 7 residues processed: 56 average time/residue: 0.0560 time to fit residues: 4.0141 Evaluate side-chains 50 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.0070 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.0000 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.0670 chunk 27 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN ** A 409 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 = 0.3847 r_free = 0.3847 target = 0.165305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.141475 restraints weight = 3781.423| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.82 r_work: 0.3412 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3268 Z= 0.117 Angle : 0.556 7.324 4471 Z= 0.282 Chirality : 0.044 0.132 503 Planarity : 0.005 0.052 570 Dihedral : 4.307 16.789 465 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.11 % Allowed : 11.71 % Favored : 84.18 % 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 (0.43), residues: 417 helix: -3.69 (1.14), residues: 12 sheet: 1.27 (0.44), residues: 144 loop : -0.19 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.010 0.001 TYR L 89 PHE 0.009 0.001 PHE A 456 TRP 0.010 0.001 TRP A 436 HIS 0.001 0.001 HIS L 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 3261) covalent geometry : angle 0.55549 / 0.28 ( 4456) SS BOND : bond 0.00199 / 0.10 ( 6) SS BOND : angle 0.61273 / 0.33 ( 12) hydrogen bonds : bond 0.03617 / 2.68 ( 103) hydrogen bonds : angle 5.81012 / 3.84 ( 258) link_NAG-ASN : bond 0.00180 / 0.09 ( 1) link_NAG-ASN : angle 0.95614 / 0.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.077 Fit side-chains REVERT: H 54 TYR cc_start: 0.8958 (m-80) cc_final: 0.8753 (m-80) REVERT: L 108 THR cc_start: 0.7830 (t) cc_final: 0.7616 (p) REVERT: A 468 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7738 (pt) outliers start: 13 outliers final: 7 residues processed: 54 average time/residue: 0.0596 time to fit residues: 3.8630 Evaluate side-chains 52 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 40 GLN A 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.158432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135506 restraints weight = 3812.183| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.72 r_work: 0.3378 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 3268 Z= 0.279 Angle : 0.720 11.328 4471 Z= 0.353 Chirality : 0.050 0.153 503 Planarity : 0.005 0.052 570 Dihedral : 5.038 21.427 465 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.06 % Allowed : 12.03 % Favored : 82.91 % 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: -0.21 (0.42), residues: 417 helix: -3.75 (1.09), residues: 12 sheet: 1.15 (0.45), residues: 136 loop : -0.68 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 493 TYR 0.015 0.002 TYR L 89 PHE 0.017 0.002 PHE A 377 TRP 0.014 0.002 TRP H 109 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.28 ( 3261) covalent geometry : angle 0.71883 / 0.35 ( 4456) SS BOND : bond 0.00259 / 0.15 ( 6) SS BOND : angle 0.73203 / 0.41 ( 12) hydrogen bonds : bond 0.04601 / 3.36 ( 103) hydrogen bonds : angle 6.24471 / 4.15 ( 258) link_NAG-ASN : bond 0.00035 / 0.02 ( 1) link_NAG-ASN : angle 1.37918 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.121 Fit side-chains REVERT: A 456 PHE cc_start: 0.9043 (m-80) cc_final: 0.8841 (m-80) outliers start: 16 outliers final: 12 residues processed: 50 average time/residue: 0.0524 time to fit residues: 3.2964 Evaluate side-chains 50 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 30 optimal weight: 0.0980 chunk 1 optimal weight: 0.0670 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.157433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133703 restraints weight = 3792.604| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.80 r_work: 0.3389 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3268 Z= 0.138 Angle : 0.578 9.015 4471 Z= 0.286 Chirality : 0.045 0.143 503 Planarity : 0.005 0.054 570 Dihedral : 4.552 17.718 465 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.75 % Allowed : 12.03 % Favored : 83.23 % 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: -0.18 (0.42), residues: 417 helix: -3.73 (1.08), residues: 12 sheet: 0.98 (0.44), residues: 144 loop : -0.58 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.010 0.001 TYR L 39 PHE 0.009 0.001 PHE A 374 TRP 0.009 0.001 TRP A 436 HIS 0.001 0.001 HIS L 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 3261) covalent geometry : angle 0.57717 / 0.29 ( 4456) SS BOND : bond 0.00197 / 0.11 ( 6) SS BOND : angle 0.56041 / 0.30 ( 12) hydrogen bonds : bond 0.03598 / 2.65 ( 103) hydrogen bonds : angle 5.90158 / 3.91 ( 258) link_NAG-ASN : bond 0.00114 / 0.06 ( 1) link_NAG-ASN : angle 1.13540 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.073 Fit side-chains REVERT: L 48 LYS cc_start: 0.9052 (ptmt) cc_final: 0.8800 (ptmm) REVERT: A 456 PHE cc_start: 0.9029 (m-80) cc_final: 0.8815 (m-80) REVERT: A 468 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7722 (pt) outliers start: 15 outliers final: 11 residues processed: 53 average time/residue: 0.0495 time to fit residues: 3.2059 Evaluate side-chains 53 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.156663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.132784 restraints weight = 3883.484| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.83 r_work: 0.3356 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3268 Z= 0.212 Angle : 0.637 10.439 4471 Z= 0.313 Chirality : 0.048 0.179 503 Planarity : 0.005 0.053 570 Dihedral : 4.741 18.925 465 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.43 % Allowed : 12.66 % Favored : 82.91 % 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: -0.30 (0.42), residues: 417 helix: -3.73 (1.07), residues: 12 sheet: 0.99 (0.44), residues: 143 loop : -0.73 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 60 TYR 0.011 0.002 TYR L 89 PHE 0.013 0.002 PHE A 377 TRP 0.010 0.002 TRP A 436 HIS 0.002 0.001 HIS L 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.21 ( 3261) covalent geometry : angle 0.63630 / 0.31 ( 4456) SS BOND : bond 0.00219 / 0.13 ( 6) SS BOND : angle 0.55759 / 0.31 ( 12) hydrogen bonds : bond 0.04039 / 2.97 ( 103) hydrogen bonds : angle 6.01441 / 3.99 ( 258) link_NAG-ASN : bond 0.00122 / 0.06 ( 1) link_NAG-ASN : angle 1.27593 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.071 Fit side-chains REVERT: A 386 LYS cc_start: 0.8256 (mttt) cc_final: 0.6533 (pttt) REVERT: A 456 PHE cc_start: 0.9065 (m-80) cc_final: 0.8827 (m-80) REVERT: A 468 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7793 (pt) outliers start: 14 outliers final: 13 residues processed: 51 average time/residue: 0.0356 time to fit residues: 2.3248 Evaluate side-chains 53 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 514 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.0470 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 11 optimal weight: 0.0020 chunk 20 optimal weight: 0.0980 chunk 36 optimal weight: 0.4980 overall best weight: 0.1084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.158177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.132733 restraints weight = 3825.754| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.99 r_work: 0.3300 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3268 Z= 0.085 Angle : 0.512 7.377 4471 Z= 0.257 Chirality : 0.044 0.142 503 Planarity : 0.004 0.054 570 Dihedral : 4.105 14.626 465 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.48 % Allowed : 13.92 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.42), residues: 417 helix: -4.06 (0.70), residues: 18 sheet: 1.31 (0.46), residues: 134 loop : -0.66 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.008 0.001 TYR H 61 PHE 0.008 0.001 PHE A 374 TRP 0.010 0.001 TRP A 436 HIS 0.001 0.000 HIS L 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 ( 3261) covalent geometry : angle 0.51148 / 0.26 ( 4456) SS BOND : bond 0.00191 / 0.10 ( 6) SS BOND : angle 0.48631 / 0.27 ( 12) hydrogen bonds : bond 0.02961 / 2.18 ( 103) hydrogen bonds : angle 5.63681 / 3.71 ( 258) link_NAG-ASN : bond 0.00142 / 0.07 ( 1) link_NAG-ASN : angle 0.83560 / 0.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.074 Fit side-chains REVERT: L 48 LYS cc_start: 0.8919 (ptmt) cc_final: 0.8650 (ptmm) REVERT: A 468 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7653 (pt) outliers start: 11 outliers final: 9 residues processed: 51 average time/residue: 0.0515 time to fit residues: 3.2809 Evaluate side-chains 55 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.0000 chunk 12 optimal weight: 0.0870 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.4162 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.159888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135724 restraints weight = 3879.683| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.87 r_work: 0.3388 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3268 Z= 0.151 Angle : 0.567 8.671 4471 Z= 0.279 Chirality : 0.045 0.143 503 Planarity : 0.005 0.054 570 Dihedral : 4.341 16.280 465 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.16 % Allowed : 14.87 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 417 helix: -4.36 (0.78), residues: 12 sheet: 1.13 (0.45), residues: 144 loop : -0.71 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 493 TYR 0.008 0.001 TYR L 39 PHE 0.009 0.001 PHE A 377 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.001 HIS L 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 3261) covalent geometry : angle 0.56642 / 0.28 ( 4456) SS BOND : bond 0.00186 / 0.11 ( 6) SS BOND : angle 0.45354 / 0.25 ( 12) hydrogen bonds : bond 0.03504 / 2.58 ( 103) hydrogen bonds : angle 5.78343 / 3.83 ( 258) link_NAG-ASN : bond 0.00095 / 0.05 ( 1) link_NAG-ASN : angle 1.06235 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.073 Fit side-chains REVERT: A 386 LYS cc_start: 0.8195 (mttt) cc_final: 0.6510 (pttt) REVERT: A 456 PHE cc_start: 0.9046 (m-80) cc_final: 0.8813 (m-80) REVERT: A 468 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7728 (pt) outliers start: 10 outliers final: 9 residues processed: 50 average time/residue: 0.0497 time to fit residues: 3.0534 Evaluate side-chains 61 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 0.0980 chunk 18 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.162230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.139686 restraints weight = 3786.879| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.70 r_work: 0.3438 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3268 Z= 0.140 Angle : 0.559 8.263 4471 Z= 0.276 Chirality : 0.045 0.138 503 Planarity : 0.004 0.054 570 Dihedral : 4.354 15.760 465 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.48 % Allowed : 14.24 % Favored : 82.28 % 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: -0.31 (0.42), residues: 417 helix: -4.37 (0.77), residues: 12 sheet: 1.10 (0.44), residues: 144 loop : -0.79 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 493 TYR 0.009 0.001 TYR H 49 PHE 0.008 0.001 PHE H 24 TRP 0.008 0.001 TRP A 436 HIS 0.001 0.001 HIS L 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 3261) covalent geometry : angle 0.55855 / 0.28 ( 4456) SS BOND : bond 0.00193 / 0.11 ( 6) SS BOND : angle 0.48866 / 0.27 ( 12) hydrogen bonds : bond 0.03438 / 2.54 ( 103) hydrogen bonds : angle 5.75957 / 3.82 ( 258) link_NAG-ASN : bond 0.00126 / 0.07 ( 1) link_NAG-ASN : angle 0.98952 / 0.54 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.089 Fit side-chains REVERT: A 386 LYS cc_start: 0.8175 (mttt) cc_final: 0.6581 (pttt) REVERT: A 456 PHE cc_start: 0.8985 (m-80) cc_final: 0.8750 (m-80) REVERT: A 468 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7737 (pt) outliers start: 11 outliers final: 9 residues processed: 58 average time/residue: 0.0464 time to fit residues: 3.4070 Evaluate side-chains 62 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 57 ASP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 4 optimal weight: 0.0770 chunk 27 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.161686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.138649 restraints weight = 3892.722| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.74 r_work: 0.3418 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3268 Z= 0.160 Angle : 0.570 9.000 4471 Z= 0.282 Chirality : 0.045 0.137 503 Planarity : 0.005 0.054 570 Dihedral : 4.434 16.621 465 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.48 % Allowed : 15.51 % Favored : 81.01 % 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: -0.38 (0.42), residues: 417 helix: -4.36 (0.76), residues: 12 sheet: 1.08 (0.44), residues: 144 loop : -0.87 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 493 TYR 0.010 0.001 TYR L 39 PHE 0.010 0.002 PHE A 377 TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS L 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 3261) covalent geometry : angle 0.56948 / 0.28 ( 4456) SS BOND : bond 0.00198 / 0.12 ( 6) SS BOND : angle 0.47778 / 0.27 ( 12) hydrogen bonds : bond 0.03555 / 2.60 ( 103) hydrogen bonds : angle 5.81243 / 3.86 ( 258) link_NAG-ASN : bond 0.00107 / 0.06 ( 1) link_NAG-ASN : angle 1.05212 / 0.57 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1029.85 seconds wall clock time: 18 minutes 23.44 seconds (1103.44 seconds total)