Starting phenix.real_space_refine on Tue Aug 4 13:31:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hed_34688/08_2026/8hed_34688.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hed_34688/08_2026/8hed_34688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hed_34688/08_2026/8hed_34688.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hed_34688/08_2026/8hed_34688.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hed_34688/08_2026/8hed_34688.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hed_34688/08_2026/8hed_34688.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hed_34688/08_2026/8hed_34688.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hed_34688/08_2026/8hed_34688.map" } resolution = 3.59 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= 0.022 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 18 5.16 5 C 2102 2.51 5 N 547 2.21 5 O 651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3318 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1578 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 815 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 105} Chain: "G" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 883 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" 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: 0.62, per 1000 atoms: 0.19 Number of scatterers: 3318 At special positions: 0 Unit cell: (79.54, 62.32, 102.5, 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 18 16.00 O 651 8.00 N 547 7.00 C 2102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.04 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 92 " distance=2.03 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 O 1 " - " NAG O 2 " NAG-ASN " NAG B 601 " - " ASN B 331 " " NAG O 1 " - " ASN B 343 " Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 119.9 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 9 sheets defined 11.7% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.666A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.546A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.506A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.765A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'F' and resid 78 through 82 removed outlier: 3.820A pdb=" N ASP F 81 " --> pdb=" O GLN F 78 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA F 82 " --> pdb=" O CYS F 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 78 through 82' Processing helix chain 'G' and resid 27 through 31 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.192A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.692A pdb=" N VAL F 18 " --> pdb=" O MET F 74 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS F 69 " --> pdb=" O SER F 66 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR F 71 " --> pdb=" O SER F 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 9 through 13 removed outlier: 3.569A pdb=" N VAL F 108 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 12 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS F 110 " --> pdb=" O ALA F 12 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE F 47 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN F 36 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU F 45 " --> pdb=" O GLN F 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 9 through 13 removed outlier: 3.569A pdb=" N VAL F 108 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 12 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS F 110 " --> pdb=" O ALA F 12 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY F 89 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA F 100 " --> pdb=" O GLY F 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'G' and resid 10 through 11 removed outlier: 7.196A pdb=" N MET G 33 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE G 49 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.981A pdb=" N PHE G 106 " --> pdb=" O ARG G 94 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 252 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: 0.30 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1054 1.35 - 1.47: 906 1.47 - 1.59: 1418 1.59 - 1.71: 0 1.71 - 1.83: 21 Bond restraints: 3399 Sorted by residual: bond pdb=" N ASN B 501 " pdb=" CA ASN B 501 " ideal model delta sigma weight residual 1.453 1.483 -0.030 1.22e-02 6.72e+03 6.06e+00 bond pdb=" N CYS F 98 " pdb=" CA CYS F 98 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.04e+00 bond pdb=" N GLU F 90 " pdb=" CA GLU F 90 " ideal model delta sigma weight residual 1.454 1.486 -0.033 1.34e-02 5.57e+03 5.97e+00 bond pdb=" N THR F 99 " pdb=" CA THR F 99 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.78e+00 bond pdb=" N CYS F 93 " pdb=" CA CYS F 93 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.47e+00 ... (remaining 3394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 4338 1.27 - 2.55: 222 2.55 - 3.82: 55 3.82 - 5.09: 7 5.09 - 6.37: 3 Bond angle restraints: 4625 Sorted by residual: angle pdb=" CA ASP F 97 " pdb=" C ASP F 97 " pdb=" O ASP F 97 " ideal model delta sigma weight residual 121.78 118.20 3.58 1.12e+00 7.97e-01 1.02e+01 angle pdb=" CA LYS G 63 " pdb=" CB LYS G 63 " pdb=" CG LYS G 63 " ideal model delta sigma weight residual 114.10 120.40 -6.30 2.00e+00 2.50e-01 9.91e+00 angle pdb=" CA GLU F 90 " pdb=" C GLU F 90 " pdb=" O GLU F 90 " ideal model delta sigma weight residual 121.87 118.35 3.52 1.16e+00 7.43e-01 9.22e+00 angle pdb=" CA ARG B 403 " pdb=" C ARG B 403 " pdb=" O ARG B 403 " ideal model delta sigma weight residual 121.87 118.71 3.16 1.10e+00 8.26e-01 8.23e+00 angle pdb=" CA PHE F 91 " pdb=" C PHE F 91 " pdb=" O PHE F 91 " ideal model delta sigma weight residual 122.31 118.61 3.70 1.31e+00 5.83e-01 7.98e+00 ... (remaining 4620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.74: 1685 14.74 - 29.48: 199 29.48 - 44.21: 60 44.21 - 58.95: 12 58.95 - 73.69: 3 Dihedral angle restraints: 1959 sinusoidal: 739 harmonic: 1220 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual -86.00 -37.18 -48.82 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 54.96 38.04 1 1.00e+01 1.00e-02 2.04e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 58.20 34.80 1 1.00e+01 1.00e-02 1.72e+01 ... (remaining 1956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 302 0.029 - 0.058: 129 0.058 - 0.087: 39 0.087 - 0.116: 41 0.116 - 0.146: 7 Chirality restraints: 518 Sorted by residual: chirality pdb=" CA LEU G 28 " pdb=" N LEU G 28 " pdb=" C LEU G 28 " pdb=" CB LEU G 28 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA PHE F 91 " pdb=" N PHE F 91 " pdb=" C PHE F 91 " pdb=" CB PHE F 91 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA PRO B 337 " pdb=" N PRO B 337 " pdb=" C PRO B 337 " pdb=" CB PRO B 337 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 515 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 63 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C LYS G 63 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS G 63 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY G 64 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 468 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C ILE B 468 " 0.020 2.00e-02 2.50e+03 pdb=" O ILE B 468 " -0.007 2.00e-02 2.50e+03 pdb=" N SER B 469 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 89 " -0.005 2.00e-02 2.50e+03 1.03e-02 1.05e+00 pdb=" C GLY F 89 " 0.018 2.00e-02 2.50e+03 pdb=" O GLY F 89 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU F 90 " -0.006 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 698 2.78 - 3.31: 2933 3.31 - 3.84: 5034 3.84 - 4.37: 5680 4.37 - 4.90: 10270 Nonbonded interactions: 24615 Sorted by model distance: nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.247 3.040 nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.247 3.040 nonbonded pdb=" N GLU B 340 " pdb=" OE1 GLU B 340 " model vdw 2.254 3.120 nonbonded pdb=" OH TYR F 35 " pdb=" O VAL G 103 " model vdw 2.318 3.040 nonbonded pdb=" OD1 ASP G 52 " pdb=" N SER G 53 " model vdw 2.360 3.120 ... (remaining 24610 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: 10.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.770 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3408 Z= 0.225 Angle : 0.680 6.368 4646 Z= 0.378 Chirality : 0.044 0.146 518 Planarity : 0.003 0.026 592 Dihedral : 13.945 73.689 1169 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.65 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 18.21 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.46 (0.42), residues: 421 helix: -2.38 (1.25), residues: 15 sheet: 1.03 (0.49), residues: 136 loop : -0.94 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 30 TYR 0.007 0.001 TYR B 495 PHE 0.007 0.001 PHE B 342 TRP 0.005 0.001 TRP G 61 HIS 0.001 0.001 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.22 ( 3399) covalent geometry : angle 0.67002 / 0.38 ( 4625) SS BOND : bond 0.00441 / 0.26 ( 6) SS BOND : angle 1.84634 / 1.18 ( 12) hydrogen bonds : bond 0.26743 / 17.53 ( 94) hydrogen bonds : angle 9.66867 / 6.83 ( 252) link_BETA1-4 : bond 0.00631 / 0.33 ( 1) link_BETA1-4 : angle 0.86024 / 0.59 ( 3) link_NAG-ASN : bond 0.00512 / 0.27 ( 2) link_NAG-ASN : angle 2.07250 / 1.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.148 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0715 time to fit residues: 5.6086 Evaluate side-chains 63 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.0980 chunk 26 optimal weight: 0.0040 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 = 0.3359 r_free = 0.3359 target = 0.079573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.069633 restraints weight = 10143.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.072014 restraints weight = 4727.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.073627 restraints weight = 2807.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.074703 restraints weight = 1896.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.075474 restraints weight = 1406.416| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3408 Z= 0.120 Angle : 0.586 8.084 4646 Z= 0.304 Chirality : 0.043 0.150 518 Planarity : 0.003 0.022 592 Dihedral : 4.231 15.541 466 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.41 % Favored : 93.35 % Rotamer: Outliers : 2.80 % Allowed : 17.93 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.42), residues: 421 helix: -1.93 (1.38), residues: 15 sheet: 1.22 (0.48), residues: 138 loop : -0.95 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 403 TYR 0.011 0.001 TYR B 453 PHE 0.008 0.001 PHE B 342 TRP 0.007 0.001 TRP B 436 HIS 0.002 0.001 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 3399) covalent geometry : angle 0.58234 / 0.30 ( 4625) SS BOND : bond 0.00508 / 0.35 ( 6) SS BOND : angle 1.05751 / 0.77 ( 12) hydrogen bonds : bond 0.05410 / 3.39 ( 94) hydrogen bonds : angle 7.09845 / 5.07 ( 252) link_BETA1-4 : bond 0.00577 / 0.30 ( 1) link_BETA1-4 : angle 1.08162 / 0.77 ( 3) link_NAG-ASN : bond 0.00494 / 0.26 ( 2) link_NAG-ASN : angle 1.40252 / 0.99 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.4250 (t0) cc_final: 0.4038 (t0) REVERT: G 52 ASP cc_start: 0.8889 (p0) cc_final: 0.8672 (p0) outliers start: 10 outliers final: 6 residues processed: 76 average time/residue: 0.0573 time to fit residues: 5.1853 Evaluate side-chains 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.077793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.067938 restraints weight = 10048.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070274 restraints weight = 4674.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.071865 restraints weight = 2770.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072952 restraints weight = 1860.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.073717 restraints weight = 1368.927| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3408 Z= 0.163 Angle : 0.593 7.141 4646 Z= 0.305 Chirality : 0.044 0.146 518 Planarity : 0.003 0.023 592 Dihedral : 4.393 15.873 466 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.36 % Favored : 92.40 % Rotamer: Outliers : 3.36 % Allowed : 19.61 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.42), residues: 421 helix: -1.61 (1.45), residues: 15 sheet: 1.27 (0.47), residues: 137 loop : -1.07 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 403 TYR 0.011 0.001 TYR B 453 PHE 0.010 0.001 PHE B 342 TRP 0.007 0.001 TRP G 46 HIS 0.002 0.001 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 3399) covalent geometry : angle 0.58605 / 0.30 ( 4625) SS BOND : bond 0.00684 / 0.43 ( 6) SS BOND : angle 1.51036 / 1.15 ( 12) hydrogen bonds : bond 0.04420 / 2.72 ( 94) hydrogen bonds : angle 6.34788 / 4.50 ( 252) link_BETA1-4 : bond 0.00658 / 0.35 ( 1) link_BETA1-4 : angle 1.14148 / 0.83 ( 3) link_NAG-ASN : bond 0.00629 / 0.33 ( 2) link_NAG-ASN : angle 1.51675 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: F 23 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7804 (tm-30) outliers start: 12 outliers final: 9 residues processed: 73 average time/residue: 0.0639 time to fit residues: 5.5374 Evaluate side-chains 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 112 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.078677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.068781 restraints weight = 9932.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.071168 restraints weight = 4603.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.072746 restraints weight = 2719.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.073839 restraints weight = 1836.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.074600 restraints weight = 1355.825| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3408 Z= 0.121 Angle : 0.566 6.457 4646 Z= 0.289 Chirality : 0.043 0.153 518 Planarity : 0.003 0.023 592 Dihedral : 4.230 15.297 466 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.70 % Favored : 94.06 % Rotamer: Outliers : 3.08 % Allowed : 20.73 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.42), residues: 421 helix: -1.67 (1.44), residues: 15 sheet: 1.15 (0.47), residues: 142 loop : -1.03 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.010 0.001 TYR B 453 PHE 0.007 0.001 PHE B 342 TRP 0.006 0.001 TRP G 46 HIS 0.002 0.001 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 3399) covalent geometry : angle 0.55944 / 0.29 ( 4625) SS BOND : bond 0.00627 / 0.38 ( 6) SS BOND : angle 1.32600 / 1.05 ( 12) hydrogen bonds : bond 0.03788 / 2.26 ( 94) hydrogen bonds : angle 5.93571 / 4.17 ( 252) link_BETA1-4 : bond 0.00635 / 0.33 ( 1) link_BETA1-4 : angle 1.16213 / 0.90 ( 3) link_NAG-ASN : bond 0.00509 / 0.27 ( 2) link_NAG-ASN : angle 1.51107 / 1.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: B 474 GLN cc_start: 0.8804 (pp30) cc_final: 0.8586 (pp30) REVERT: B 487 ASN cc_start: 0.3862 (t0) cc_final: 0.3614 (t0) outliers start: 11 outliers final: 8 residues processed: 80 average time/residue: 0.0670 time to fit residues: 6.3653 Evaluate side-chains 77 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.078429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.068566 restraints weight = 9937.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.070929 restraints weight = 4626.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.072516 restraints weight = 2727.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.073531 restraints weight = 1838.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074292 restraints weight = 1374.917| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3408 Z= 0.131 Angle : 0.581 6.449 4646 Z= 0.296 Chirality : 0.043 0.150 518 Planarity : 0.003 0.023 592 Dihedral : 4.293 15.335 466 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.84 % Favored : 91.92 % Rotamer: Outliers : 4.76 % Allowed : 19.61 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.43), residues: 421 helix: -1.63 (1.47), residues: 15 sheet: 1.25 (0.47), residues: 141 loop : -1.07 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.011 0.001 TYR B 453 PHE 0.008 0.001 PHE B 342 TRP 0.006 0.001 TRP G 46 HIS 0.001 0.001 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 3399) covalent geometry : angle 0.57183 / 0.29 ( 4625) SS BOND : bond 0.00521 / 0.35 ( 6) SS BOND : angle 1.80564 / 1.25 ( 12) hydrogen bonds : bond 0.03626 / 2.20 ( 94) hydrogen bonds : angle 5.74522 / 4.05 ( 252) link_BETA1-4 : bond 0.00590 / 0.31 ( 1) link_BETA1-4 : angle 1.13502 / 0.85 ( 3) link_NAG-ASN : bond 0.00522 / 0.27 ( 2) link_NAG-ASN : angle 1.55062 / 1.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.089 Fit side-chains revert: symmetry clash REVERT: B 474 GLN cc_start: 0.8800 (pp30) cc_final: 0.8571 (pp30) REVERT: B 487 ASN cc_start: 0.3958 (t0) cc_final: 0.3703 (t0) REVERT: F 23 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7766 (tm-30) outliers start: 17 outliers final: 11 residues processed: 85 average time/residue: 0.0705 time to fit residues: 7.0846 Evaluate side-chains 82 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.077394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.067661 restraints weight = 9909.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.069978 restraints weight = 4557.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.071533 restraints weight = 2679.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.072580 restraints weight = 1799.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.073330 restraints weight = 1328.351| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3408 Z= 0.156 Angle : 0.591 8.359 4646 Z= 0.303 Chirality : 0.044 0.150 518 Planarity : 0.003 0.023 592 Dihedral : 4.468 20.495 466 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.92 % Allowed : 19.61 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.41 (0.42), residues: 421 helix: -1.58 (1.46), residues: 15 sheet: 1.31 (0.47), residues: 140 loop : -1.16 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.011 0.001 TYR B 453 PHE 0.010 0.001 PHE G 91 TRP 0.006 0.001 TRP G 46 HIS 0.002 0.001 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 3399) covalent geometry : angle 0.58226 / 0.30 ( 4625) SS BOND : bond 0.00769 / 0.47 ( 6) SS BOND : angle 1.62530 / 1.18 ( 12) hydrogen bonds : bond 0.03661 / 2.18 ( 94) hydrogen bonds : angle 5.69953 / 4.02 ( 252) link_BETA1-4 : bond 0.00589 / 0.31 ( 1) link_BETA1-4 : angle 1.23650 / 0.89 ( 3) link_NAG-ASN : bond 0.00625 / 0.33 ( 2) link_NAG-ASN : angle 1.62975 / 1.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.4043 (t0) cc_final: 0.3761 (t0) REVERT: F 23 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7763 (tm-30) REVERT: F 35 TYR cc_start: 0.9222 (m-80) cc_final: 0.9001 (m-80) outliers start: 14 outliers final: 11 residues processed: 78 average time/residue: 0.0638 time to fit residues: 5.9459 Evaluate side-chains 80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.0040 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 = 0.3323 r_free = 0.3323 target = 0.077769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.067992 restraints weight = 10134.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070323 restraints weight = 4672.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.071894 restraints weight = 2737.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.072952 restraints weight = 1833.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.073685 restraints weight = 1347.735| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3408 Z= 0.136 Angle : 0.606 7.545 4646 Z= 0.305 Chirality : 0.043 0.150 518 Planarity : 0.003 0.023 592 Dihedral : 4.383 17.943 466 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.36 % Allowed : 21.29 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.42), residues: 421 helix: -1.71 (1.43), residues: 15 sheet: 1.31 (0.47), residues: 140 loop : -1.17 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 30 TYR 0.011 0.001 TYR B 453 PHE 0.008 0.001 PHE G 91 TRP 0.006 0.001 TRP G 46 HIS 0.001 0.000 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 3399) covalent geometry : angle 0.59861 / 0.30 ( 4625) SS BOND : bond 0.00682 / 0.42 ( 6) SS BOND : angle 1.46355 / 1.13 ( 12) hydrogen bonds : bond 0.03542 / 2.08 ( 94) hydrogen bonds : angle 5.58901 / 3.94 ( 252) link_BETA1-4 : bond 0.00642 / 0.34 ( 1) link_BETA1-4 : angle 1.25858 / 0.95 ( 3) link_NAG-ASN : bond 0.00537 / 0.28 ( 2) link_NAG-ASN : angle 1.62806 / 1.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.4012 (t0) cc_final: 0.3764 (t0) REVERT: F 35 TYR cc_start: 0.9189 (m-80) cc_final: 0.8977 (m-80) REVERT: F 62 ARG cc_start: 0.7927 (tmm-80) cc_final: 0.7650 (mtp180) outliers start: 12 outliers final: 10 residues processed: 78 average time/residue: 0.0658 time to fit residues: 6.0933 Evaluate side-chains 79 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 38 optimal weight: 0.0870 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.078029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068330 restraints weight = 10087.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.070670 restraints weight = 4625.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.072238 restraints weight = 2691.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.073269 restraints weight = 1795.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.073994 restraints weight = 1327.942| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3408 Z= 0.131 Angle : 0.626 7.992 4646 Z= 0.311 Chirality : 0.043 0.149 518 Planarity : 0.003 0.023 592 Dihedral : 4.330 16.597 466 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.64 % Allowed : 21.01 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.44 (0.42), residues: 421 helix: -1.74 (1.42), residues: 15 sheet: 1.34 (0.46), residues: 146 loop : -1.26 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.010 0.001 TYR B 453 PHE 0.008 0.001 PHE B 342 TRP 0.006 0.001 TRP G 46 HIS 0.001 0.001 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 3399) covalent geometry : angle 0.62019 / 0.31 ( 4625) SS BOND : bond 0.00634 / 0.39 ( 6) SS BOND : angle 1.33050 / 1.02 ( 12) hydrogen bonds : bond 0.03502 / 2.04 ( 94) hydrogen bonds : angle 5.53884 / 3.90 ( 252) link_BETA1-4 : bond 0.00637 / 0.34 ( 1) link_BETA1-4 : angle 1.23449 / 0.94 ( 3) link_NAG-ASN : bond 0.00506 / 0.27 ( 2) link_NAG-ASN : angle 1.63132 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: B 487 ASN cc_start: 0.3977 (t0) cc_final: 0.3740 (t0) REVERT: F 23 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7707 (tm-30) outliers start: 13 outliers final: 12 residues processed: 80 average time/residue: 0.0702 time to fit residues: 6.6161 Evaluate side-chains 81 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 18 optimal weight: 0.0070 chunk 36 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 overall best weight: 0.3398 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.079094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.069242 restraints weight = 9894.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.071647 restraints weight = 4541.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.073264 restraints weight = 2649.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.074321 restraints weight = 1767.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.075067 restraints weight = 1305.387| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3408 Z= 0.113 Angle : 0.620 8.251 4646 Z= 0.307 Chirality : 0.043 0.149 518 Planarity : 0.003 0.022 592 Dihedral : 4.171 15.205 466 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.36 % Allowed : 21.85 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.42), residues: 421 helix: -2.75 (1.06), residues: 21 sheet: 1.33 (0.45), residues: 146 loop : -1.17 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.012 0.001 TYR B 369 PHE 0.007 0.001 PHE B 342 TRP 0.006 0.001 TRP G 46 HIS 0.001 0.000 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 3399) covalent geometry : angle 0.61471 / 0.31 ( 4625) SS BOND : bond 0.00584 / 0.35 ( 6) SS BOND : angle 1.20275 / 0.93 ( 12) hydrogen bonds : bond 0.03398 / 1.96 ( 94) hydrogen bonds : angle 5.39529 / 3.79 ( 252) link_BETA1-4 : bond 0.00598 / 0.31 ( 1) link_BETA1-4 : angle 1.13658 / 0.90 ( 3) link_NAG-ASN : bond 0.00402 / 0.21 ( 2) link_NAG-ASN : angle 1.60565 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: B 474 GLN cc_start: 0.8754 (pp30) cc_final: 0.8508 (pp30) REVERT: F 23 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7699 (tm-30) REVERT: F 62 ARG cc_start: 0.7943 (tmm-80) cc_final: 0.7604 (mtp180) outliers start: 12 outliers final: 11 residues processed: 83 average time/residue: 0.0665 time to fit residues: 6.5483 Evaluate side-chains 80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 9 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.5058 > 50:) chunk 31 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 19 optimal weight: 0.0370 overall best weight: 0.3058 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.079618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.069572 restraints weight = 9913.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.072027 restraints weight = 4560.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.073639 restraints weight = 2663.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.074736 restraints weight = 1787.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.075440 restraints weight = 1317.147| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3408 Z= 0.116 Angle : 0.636 8.310 4646 Z= 0.319 Chirality : 0.044 0.181 518 Planarity : 0.003 0.022 592 Dihedral : 4.149 16.331 466 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.08 % Allowed : 21.57 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.51 (0.42), residues: 421 helix: -2.75 (1.06), residues: 21 sheet: 1.32 (0.45), residues: 145 loop : -1.20 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 403 TYR 0.008 0.001 TYR B 453 PHE 0.009 0.001 PHE B 486 TRP 0.005 0.001 TRP G 61 HIS 0.001 0.000 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.11 ( 3399) covalent geometry : angle 0.63107 / 0.32 ( 4625) SS BOND : bond 0.00601 / 0.35 ( 6) SS BOND : angle 1.28240 / 0.92 ( 12) hydrogen bonds : bond 0.03343 / 1.92 ( 94) hydrogen bonds : angle 5.35224 / 3.76 ( 252) link_BETA1-4 : bond 0.00617 / 0.32 ( 1) link_BETA1-4 : angle 1.10419 / 0.88 ( 3) link_NAG-ASN : bond 0.00389 / 0.20 ( 2) link_NAG-ASN : angle 1.61563 / 1.17 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: B 474 GLN cc_start: 0.8814 (pp30) cc_final: 0.8435 (pp30) REVERT: F 23 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7700 (tm-30) REVERT: F 62 ARG cc_start: 0.7974 (tmm-80) cc_final: 0.7642 (mtp180) REVERT: G 4 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7614 (tm-30) outliers start: 11 outliers final: 10 residues processed: 76 average time/residue: 0.0705 time to fit residues: 6.3607 Evaluate side-chains 80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 GLN Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.0370 chunk 8 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 overall best weight: 0.2394 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.079907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.069975 restraints weight = 9901.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.072420 restraints weight = 4548.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.073979 restraints weight = 2649.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.075098 restraints weight = 1792.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.075847 restraints weight = 1309.985| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3408 Z= 0.109 Angle : 0.634 8.995 4646 Z= 0.314 Chirality : 0.043 0.146 518 Planarity : 0.003 0.022 592 Dihedral : 4.064 15.815 466 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.80 % Allowed : 22.69 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.46 (0.42), residues: 421 helix: -2.71 (1.08), residues: 21 sheet: 1.31 (0.45), residues: 145 loop : -1.14 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.014 0.001 TYR B 369 PHE 0.006 0.001 PHE G 91 TRP 0.006 0.001 TRP G 61 HIS 0.001 0.000 HIS G 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 3399) covalent geometry : angle 0.62893 / 0.31 ( 4625) SS BOND : bond 0.00565 / 0.33 ( 6) SS BOND : angle 1.16660 / 0.88 ( 12) hydrogen bonds : bond 0.03265 / 1.85 ( 94) hydrogen bonds : angle 5.24281 / 3.67 ( 252) link_BETA1-4 : bond 0.00616 / 0.32 ( 1) link_BETA1-4 : angle 1.08022 / 0.87 ( 3) link_NAG-ASN : bond 0.00346 / 0.18 ( 2) link_NAG-ASN : angle 1.60833 / 1.17 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 779.64 seconds wall clock time: 14 minutes 4.35 seconds (844.35 seconds total)