Starting phenix.real_space_refine on Thu Jul 2 00:25:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dad_27270/07_2026/8dad_27270.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dad_27270/07_2026/8dad_27270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dad_27270/07_2026/8dad_27270.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dad_27270/07_2026/8dad_27270.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dad_27270/07_2026/8dad_27270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dad_27270/07_2026/8dad_27270.map" model { file = "/net/cci-nas-00/data/ceres_data/8dad_27270/07_2026/8dad_27270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dad_27270/07_2026/8dad_27270.cif" } resolution = 3.85 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= -0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1656 atoms to isotropic. 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 19 5.16 5 C 2068 2.51 5 N 558 2.21 5 O 610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 3255 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1428 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 5, 'GLN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "J" 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: "A" 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 Time building chain proxies: 0.60, per 1000 atoms: 0.18 Number of scatterers: 3255 At special positions: 0 Unit cell: (62.83, 64.89, 101.97, 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 19 16.00 O 610 8.00 N 558 7.00 C 2068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 A 1 " - " NAG A 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 0.20 Conformation dependent library (CDL) restraints added in 76.3 milliseconds 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 12.0% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.898A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.194A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.215A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.585A pdb=" N MET H 112 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.638A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 121 hydrogen bonds defined for protein. 285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.44 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1052 1.34 - 1.46: 889 1.46 - 1.58: 1371 1.58 - 1.70: 0 1.70 - 1.83: 24 Bond restraints: 3336 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" C1 NAG J 1 " pdb=" C2 NAG J 1 " ideal model delta sigma weight residual 1.532 1.506 0.026 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C5 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.413 1.439 -0.026 2.00e-02 2.50e+03 1.72e+00 ... (remaining 3331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 4452 2.54 - 5.09: 78 5.09 - 7.63: 11 7.63 - 10.17: 1 10.17 - 12.72: 2 Bond angle restraints: 4544 Sorted by residual: angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 107.69 120.41 -12.72 2.01e+00 2.48e-01 4.00e+01 angle pdb=" N LEU B 390 " pdb=" CA LEU B 390 " pdb=" C LEU B 390 " ideal model delta sigma weight residual 109.76 115.86 -6.10 1.59e+00 3.96e-01 1.47e+01 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 122.98 -8.58 2.30e+00 1.89e-01 1.39e+01 angle pdb=" CB MET H 118 " pdb=" CG MET H 118 " pdb=" SD MET H 118 " ideal model delta sigma weight residual 112.70 123.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA CYS B 525 " pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " ideal model delta sigma weight residual 114.40 121.52 -7.12 2.30e+00 1.89e-01 9.57e+00 ... (remaining 4539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 1660 16.48 - 32.96: 205 32.96 - 49.44: 51 49.44 - 65.91: 10 65.91 - 82.39: 7 Dihedral angle restraints: 1933 sinusoidal: 707 harmonic: 1226 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -166.15 80.15 1 1.00e+01 1.00e-02 7.96e+01 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 93.00 19.42 73.58 1 1.00e+01 1.00e-02 6.89e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 164.39 -71.39 1 1.00e+01 1.00e-02 6.54e+01 ... (remaining 1930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 477 0.106 - 0.212: 23 0.212 - 0.318: 0 0.318 - 0.424: 0 0.424 - 0.529: 1 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA CYS B 391 " pdb=" N CYS B 391 " pdb=" C CYS B 391 " pdb=" CB CYS B 391 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" C4 NAG J 1 " pdb=" C3 NAG J 1 " pdb=" C5 NAG J 1 " pdb=" O4 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 7.44e-01 ... (remaining 498 not shown) Planarity restraints: 589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 36 " -0.012 2.00e-02 2.50e+03 1.85e-02 8.60e+00 pdb=" CG TRP L 36 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP L 36 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP L 36 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP L 36 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP L 36 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP L 36 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 36 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 36 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 36 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY H 8 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.61e+00 pdb=" N PRO H 9 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO H 9 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 9 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 527 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " -0.022 5.00e-02 4.00e+02 ... (remaining 586 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 631 2.77 - 3.30: 3114 3.30 - 3.84: 5612 3.84 - 4.37: 6247 4.37 - 4.90: 10905 Nonbonded interactions: 26509 Sorted by model distance: nonbonded pdb=" N GLU H 66 " pdb=" OE1 GLU H 66 " model vdw 2.238 3.120 nonbonded pdb=" OH TYR L 37 " pdb=" OE1 GLN L 90 " model vdw 2.287 3.040 nonbonded pdb=" O THR H 104 " pdb=" OH TYR B 473 " model vdw 2.293 3.040 nonbonded pdb=" OD2 ASP H 108 " pdb=" NH1 ARG L 54 " model vdw 2.310 3.120 nonbonded pdb=" N GLN H 65 " pdb=" OE1 GLN H 65 " model vdw 2.317 3.120 ... (remaining 26504 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'J' } 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: 1.940 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: 0.030 Check model and map are aligned: 0.020 Set scattering table: 0.000 Process input model: 3.770 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 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 3346 Z= 0.201 Angle : 0.846 12.716 4567 Z= 0.434 Chirality : 0.054 0.529 501 Planarity : 0.006 0.054 588 Dihedral : 15.937 82.392 1132 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.63 % Allowed : 26.98 % Favored : 72.38 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 9.52 % 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: -0.96 (0.42), residues: 418 helix: -2.01 (0.96), residues: 33 sheet: -0.55 (0.44), residues: 146 loop : -0.37 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 38 TYR 0.009 0.001 TYR L 92 PHE 0.013 0.002 PHE H 27 TRP 0.049 0.003 TRP L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 ( 3336) covalent geometry : angle 0.83189 / 0.43 ( 4544) SS BOND : bond 0.00269 / 0.14 ( 7) SS BOND : angle 2.79015 / 1.68 ( 14) hydrogen bonds : bond 0.13761 / 8.52 ( 114) hydrogen bonds : angle 8.19943 / 5.62 ( 285) link_BETA1-4 : bond 0.00337 / 0.17 ( 2) link_BETA1-4 : angle 0.81715 / 0.59 ( 6) link_NAG-ASN : bond 0.00118 / 0.06 ( 1) link_NAG-ASN : angle 1.84508 / 1.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 424 LYS cc_start: 0.8407 (ttpp) cc_final: 0.8126 (ttpp) outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 0.0822 time to fit residues: 7.5863 Evaluate side-chains 72 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.112372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.093038 restraints weight = 8862.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.095650 restraints weight = 5990.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.097648 restraints weight = 4578.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.099081 restraints weight = 3729.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100030 restraints weight = 3198.303| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3346 Z= 0.138 Angle : 0.653 6.840 4567 Z= 0.335 Chirality : 0.047 0.159 501 Planarity : 0.005 0.049 588 Dihedral : 4.832 28.526 472 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.17 % Allowed : 25.08 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.91 (0.42), residues: 418 helix: -2.05 (0.97), residues: 34 sheet: -0.72 (0.41), residues: 158 loop : -0.11 (0.44), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 346 TYR 0.010 0.001 TYR L 92 PHE 0.031 0.002 PHE B 392 TRP 0.038 0.003 TRP L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 3336) covalent geometry : angle 0.64756 / 0.33 ( 4544) SS BOND : bond 0.00567 / 0.25 ( 7) SS BOND : angle 1.58268 / 0.93 ( 14) hydrogen bonds : bond 0.03446 / 2.29 ( 114) hydrogen bonds : angle 6.78098 / 4.70 ( 285) link_BETA1-4 : bond 0.00210 / 0.10 ( 2) link_BETA1-4 : angle 0.85129 / 0.61 ( 6) link_NAG-ASN : bond 0.00119 / 0.06 ( 1) link_NAG-ASN : angle 1.25343 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8019 (t60) cc_final: 0.7628 (t60) REVERT: H 112 MET cc_start: 0.8184 (mpp) cc_final: 0.6985 (mpp) REVERT: L 78 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7786 (tmm160) REVERT: L 80 GLU cc_start: 0.7355 (tt0) cc_final: 0.7041 (tt0) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 0.0601 time to fit residues: 6.1719 Evaluate side-chains 76 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 29 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.0870 chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.113680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.095587 restraints weight = 8642.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.098124 restraints weight = 6027.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.099909 restraints weight = 4622.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.101190 restraints weight = 3809.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.102297 restraints weight = 3287.695| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3346 Z= 0.112 Angle : 0.671 9.397 4567 Z= 0.335 Chirality : 0.046 0.151 501 Planarity : 0.005 0.047 588 Dihedral : 4.651 24.077 472 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.81 % Allowed : 25.40 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.85 (0.42), residues: 418 helix: -2.44 (0.86), residues: 34 sheet: -0.62 (0.41), residues: 155 loop : -0.06 (0.44), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.009 0.001 TYR L 88 PHE 0.026 0.002 PHE B 392 TRP 0.021 0.001 TRP L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 3336) covalent geometry : angle 0.65644 / 0.33 ( 4544) SS BOND : bond 0.00318 / 0.14 ( 7) SS BOND : angle 2.49181 / 1.37 ( 14) hydrogen bonds : bond 0.03267 / 2.18 ( 114) hydrogen bonds : angle 6.47338 / 4.49 ( 285) link_BETA1-4 : bond 0.00282 / 0.14 ( 2) link_BETA1-4 : angle 0.83662 / 0.61 ( 6) link_NAG-ASN : bond 0.00049 / 0.03 ( 1) link_NAG-ASN : angle 1.21342 / 0.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 36 TRP cc_start: 0.8829 (m100) cc_final: 0.8533 (m100) REVERT: H 39 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7738 (tm-30) REVERT: H 47 TRP cc_start: 0.8154 (t60) cc_final: 0.7639 (t60) REVERT: L 17 GLU cc_start: 0.6849 (pm20) cc_final: 0.6159 (pm20) REVERT: L 80 GLU cc_start: 0.7260 (tt0) cc_final: 0.6981 (tt0) REVERT: L 83 ASP cc_start: 0.7996 (m-30) cc_final: 0.7687 (m-30) outliers start: 12 outliers final: 5 residues processed: 90 average time/residue: 0.0723 time to fit residues: 7.7130 Evaluate side-chains 75 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.111407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.092913 restraints weight = 8583.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.095443 restraints weight = 5867.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.097281 restraints weight = 4470.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.098653 restraints weight = 3666.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.099756 restraints weight = 3163.064| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3346 Z= 0.188 Angle : 0.646 5.461 4567 Z= 0.333 Chirality : 0.047 0.165 501 Planarity : 0.007 0.129 588 Dihedral : 4.595 15.956 471 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.40 % Allowed : 24.13 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.84 (0.42), residues: 418 helix: -2.30 (0.90), residues: 33 sheet: -0.72 (0.40), residues: 158 loop : 0.02 (0.44), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 346 TYR 0.010 0.001 TYR B 453 PHE 0.024 0.002 PHE B 392 TRP 0.028 0.002 TRP L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 ( 3336) covalent geometry : angle 0.63946 / 0.33 ( 4544) SS BOND : bond 0.00379 / 0.18 ( 7) SS BOND : angle 1.63987 / 1.01 ( 14) hydrogen bonds : bond 0.03441 / 2.30 ( 114) hydrogen bonds : angle 6.43165 / 4.49 ( 285) link_BETA1-4 : bond 0.00258 / 0.13 ( 2) link_BETA1-4 : angle 0.89621 / 0.66 ( 6) link_NAG-ASN : bond 0.00022 / 0.01 ( 1) link_NAG-ASN : angle 1.54028 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8241 (t60) cc_final: 0.7597 (t60) REVERT: H 72 ARG cc_start: 0.7884 (pmt-80) cc_final: 0.7652 (pmt-80) REVERT: H 112 MET cc_start: 0.8301 (mpp) cc_final: 0.7805 (mpp) REVERT: L 17 GLU cc_start: 0.7152 (pm20) cc_final: 0.6352 (pm20) outliers start: 17 outliers final: 13 residues processed: 82 average time/residue: 0.0729 time to fit residues: 7.1285 Evaluate side-chains 82 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.3980 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.112467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094741 restraints weight = 8490.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097192 restraints weight = 5930.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.099035 restraints weight = 4551.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.100408 restraints weight = 3733.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.101422 restraints weight = 3203.037| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3346 Z= 0.137 Angle : 0.666 8.041 4567 Z= 0.334 Chirality : 0.046 0.161 501 Planarity : 0.006 0.095 588 Dihedral : 4.543 14.959 471 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.40 % Allowed : 24.44 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.70 (0.42), residues: 418 helix: -2.34 (0.89), residues: 33 sheet: -0.50 (0.41), residues: 155 loop : 0.02 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 78 TYR 0.008 0.001 TYR L 88 PHE 0.015 0.002 PHE B 392 TRP 0.022 0.002 TRP L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 3336) covalent geometry : angle 0.65190 / 0.33 ( 4544) SS BOND : bond 0.00283 / 0.12 ( 7) SS BOND : angle 2.46284 / 1.38 ( 14) hydrogen bonds : bond 0.03335 / 2.22 ( 114) hydrogen bonds : angle 6.32383 / 4.41 ( 285) link_BETA1-4 : bond 0.00299 / 0.14 ( 2) link_BETA1-4 : angle 0.86920 / 0.62 ( 6) link_NAG-ASN : bond 0.00016 / 0.01 ( 1) link_NAG-ASN : angle 1.43703 / 0.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8212 (t60) cc_final: 0.8009 (t60) REVERT: H 72 ARG cc_start: 0.7870 (pmt-80) cc_final: 0.7615 (pmt-80) REVERT: H 112 MET cc_start: 0.8333 (mpp) cc_final: 0.7901 (mpp) REVERT: L 11 LEU cc_start: 0.8180 (mm) cc_final: 0.7861 (mm) REVERT: L 17 GLU cc_start: 0.6922 (pm20) cc_final: 0.6212 (pm20) outliers start: 17 outliers final: 14 residues processed: 86 average time/residue: 0.0629 time to fit residues: 6.4703 Evaluate side-chains 86 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN ** L 43 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 = 0.3843 r_free = 0.3843 target = 0.111886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.092977 restraints weight = 8878.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.095652 restraints weight = 6016.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.097604 restraints weight = 4539.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.099088 restraints weight = 3693.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.100108 restraints weight = 3149.529| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3346 Z= 0.137 Angle : 0.663 8.029 4567 Z= 0.335 Chirality : 0.046 0.160 501 Planarity : 0.007 0.137 588 Dihedral : 4.529 17.061 471 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.71 % Allowed : 24.76 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.60 (0.42), residues: 418 helix: -2.39 (0.86), residues: 33 sheet: -0.34 (0.42), residues: 145 loop : 0.00 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 78 TYR 0.015 0.001 TYR H 80 PHE 0.015 0.002 PHE H 29 TRP 0.027 0.002 TRP L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 3336) covalent geometry : angle 0.65070 / 0.33 ( 4544) SS BOND : bond 0.00199 / 0.09 ( 7) SS BOND : angle 2.28217 / 1.33 ( 14) hydrogen bonds : bond 0.03363 / 2.22 ( 114) hydrogen bonds : angle 6.30520 / 4.41 ( 285) link_BETA1-4 : bond 0.00301 / 0.15 ( 2) link_BETA1-4 : angle 0.84850 / 0.61 ( 6) link_NAG-ASN : bond 0.00017 / 0.01 ( 1) link_NAG-ASN : angle 1.41253 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8248 (t60) cc_final: 0.8044 (t60) REVERT: H 72 ARG cc_start: 0.7989 (pmt-80) cc_final: 0.7671 (pmt-80) REVERT: H 112 MET cc_start: 0.8310 (mpp) cc_final: 0.7802 (mpp) REVERT: L 11 LEU cc_start: 0.8268 (mm) cc_final: 0.8020 (mm) REVERT: L 17 GLU cc_start: 0.7334 (pm20) cc_final: 0.6531 (pm20) REVERT: L 22 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.8052 (p) outliers start: 18 outliers final: 16 residues processed: 88 average time/residue: 0.0710 time to fit residues: 7.4397 Evaluate side-chains 91 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.108799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.091028 restraints weight = 8721.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.093316 restraints weight = 6295.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.094919 restraints weight = 4924.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.095698 restraints weight = 4137.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.096965 restraints weight = 3713.153| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 3346 Z= 0.281 Angle : 0.751 9.217 4567 Z= 0.384 Chirality : 0.049 0.180 501 Planarity : 0.007 0.119 588 Dihedral : 5.080 17.983 471 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 7.30 % Allowed : 24.13 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.95 (0.42), residues: 418 helix: -2.36 (0.89), residues: 33 sheet: -0.66 (0.42), residues: 152 loop : -0.20 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 78 TYR 0.015 0.002 TYR B 453 PHE 0.022 0.003 PHE H 27 TRP 0.036 0.003 TRP L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00628 / 0.28 ( 3336) covalent geometry : angle 0.74501 / 0.38 ( 4544) SS BOND : bond 0.00362 / 0.19 ( 7) SS BOND : angle 1.53153 / 1.04 ( 14) hydrogen bonds : bond 0.04044 / 2.64 ( 114) hydrogen bonds : angle 6.62544 / 4.64 ( 285) link_BETA1-4 : bond 0.00110 / 0.05 ( 2) link_BETA1-4 : angle 0.82740 / 0.55 ( 6) link_NAG-ASN : bond 0.00171 / 0.09 ( 1) link_NAG-ASN : angle 2.19121 / 1.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.7874 (ttt180) cc_final: 0.7495 (ttp80) REVERT: H 47 TRP cc_start: 0.8548 (t60) cc_final: 0.7974 (t60) REVERT: H 112 MET cc_start: 0.8506 (mpp) cc_final: 0.8011 (mpp) REVERT: L 11 LEU cc_start: 0.8248 (mm) cc_final: 0.7936 (mm) REVERT: L 22 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.8088 (p) outliers start: 23 outliers final: 18 residues processed: 85 average time/residue: 0.0647 time to fit residues: 6.5003 Evaluate side-chains 86 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 0.0010 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.109142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.090233 restraints weight = 8728.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.092976 restraints weight = 5687.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.094953 restraints weight = 4220.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.096376 restraints weight = 3399.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.097554 restraints weight = 2892.419| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3346 Z= 0.158 Angle : 0.722 8.644 4567 Z= 0.358 Chirality : 0.048 0.184 501 Planarity : 0.006 0.083 588 Dihedral : 4.899 16.163 471 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 6.35 % Allowed : 26.03 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.74 (0.42), residues: 418 helix: -2.42 (0.85), residues: 33 sheet: -0.47 (0.42), residues: 147 loop : -0.08 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 84 TYR 0.010 0.001 TYR L 88 PHE 0.018 0.002 PHE B 456 TRP 0.034 0.002 TRP L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 3336) covalent geometry : angle 0.70943 / 0.35 ( 4544) SS BOND : bond 0.00191 / 0.10 ( 7) SS BOND : angle 2.43198 / 1.38 ( 14) hydrogen bonds : bond 0.03588 / 2.32 ( 114) hydrogen bonds : angle 6.47830 / 4.54 ( 285) link_BETA1-4 : bond 0.00224 / 0.11 ( 2) link_BETA1-4 : angle 0.82768 / 0.60 ( 6) link_NAG-ASN : bond 0.00093 / 0.05 ( 1) link_NAG-ASN : angle 1.78148 / 1.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: H 47 TRP cc_start: 0.8379 (t60) cc_final: 0.7618 (t60) REVERT: H 91 THR cc_start: 0.8260 (m) cc_final: 0.8050 (m) REVERT: H 112 MET cc_start: 0.8456 (mpp) cc_final: 0.7901 (mpp) outliers start: 20 outliers final: 17 residues processed: 90 average time/residue: 0.0652 time to fit residues: 6.9140 Evaluate side-chains 88 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.111255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.093729 restraints weight = 8699.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.095976 restraints weight = 6198.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.097641 restraints weight = 4861.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.098919 restraints weight = 4054.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.099883 restraints weight = 3519.213| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3346 Z= 0.159 Angle : 0.725 7.073 4567 Z= 0.365 Chirality : 0.048 0.178 501 Planarity : 0.005 0.049 588 Dihedral : 4.922 22.663 471 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.40 % Allowed : 27.30 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.79 (0.43), residues: 418 helix: -2.59 (0.83), residues: 33 sheet: -0.48 (0.42), residues: 151 loop : -0.10 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 87 TYR 0.010 0.001 TYR L 88 PHE 0.015 0.002 PHE H 27 TRP 0.054 0.003 TRP L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 3336) covalent geometry : angle 0.71692 / 0.36 ( 4544) SS BOND : bond 0.00318 / 0.14 ( 7) SS BOND : angle 1.90416 / 1.20 ( 14) hydrogen bonds : bond 0.03587 / 2.34 ( 114) hydrogen bonds : angle 6.39421 / 4.46 ( 285) link_BETA1-4 : bond 0.00255 / 0.13 ( 2) link_BETA1-4 : angle 0.82782 / 0.62 ( 6) link_NAG-ASN : bond 0.00029 / 0.02 ( 1) link_NAG-ASN : angle 1.67673 / 0.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: H 91 THR cc_start: 0.8157 (m) cc_final: 0.7933 (m) REVERT: H 112 MET cc_start: 0.8458 (mpp) cc_final: 0.8028 (mpp) outliers start: 17 outliers final: 17 residues processed: 83 average time/residue: 0.0729 time to fit residues: 7.3435 Evaluate side-chains 88 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 0 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.111111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.092291 restraints weight = 8739.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.094942 restraints weight = 5845.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.096901 restraints weight = 4421.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.098377 restraints weight = 3601.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.099497 restraints weight = 3072.421| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3346 Z= 0.144 Angle : 0.733 11.211 4567 Z= 0.363 Chirality : 0.048 0.177 501 Planarity : 0.005 0.050 588 Dihedral : 4.823 17.607 471 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.08 % Allowed : 28.25 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.76 (0.43), residues: 418 helix: -2.56 (0.83), residues: 33 sheet: -0.50 (0.42), residues: 149 loop : -0.04 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 87 TYR 0.009 0.001 TYR L 88 PHE 0.014 0.002 PHE H 27 TRP 0.053 0.003 TRP L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 3336) covalent geometry : angle 0.72222 / 0.36 ( 4544) SS BOND : bond 0.00400 / 0.15 ( 7) SS BOND : angle 2.30347 / 1.34 ( 14) hydrogen bonds : bond 0.03499 / 2.29 ( 114) hydrogen bonds : angle 6.36609 / 4.46 ( 285) link_BETA1-4 : bond 0.00292 / 0.14 ( 2) link_BETA1-4 : angle 0.85748 / 0.63 ( 6) link_NAG-ASN : bond 0.00014 / 0.01 ( 1) link_NAG-ASN : angle 1.59657 / 0.93 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 836 Ramachandran restraints generated. 418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: H 46 GLU cc_start: 0.6694 (pm20) cc_final: 0.6479 (pm20) REVERT: H 47 TRP cc_start: 0.8331 (t60) cc_final: 0.7729 (t60) REVERT: H 91 THR cc_start: 0.8250 (m) cc_final: 0.8032 (m) REVERT: H 112 MET cc_start: 0.8422 (mpp) cc_final: 0.7899 (mpp) outliers start: 16 outliers final: 16 residues processed: 83 average time/residue: 0.0498 time to fit residues: 5.0767 Evaluate side-chains 87 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.111180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.092378 restraints weight = 8876.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.095020 restraints weight = 5912.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.096882 restraints weight = 4481.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.098380 restraints weight = 3691.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.099461 restraints weight = 3148.744| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3346 Z= 0.142 Angle : 0.727 7.424 4567 Z= 0.364 Chirality : 0.047 0.173 501 Planarity : 0.005 0.050 588 Dihedral : 4.691 16.721 471 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 6.03 % Allowed : 28.25 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.80 (0.43), residues: 418 helix: -2.57 (0.83), residues: 33 sheet: -0.64 (0.40), residues: 161 loop : 0.06 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 87 TYR 0.024 0.001 TYR H 80 PHE 0.015 0.002 PHE H 27 TRP 0.048 0.003 TRP L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 3336) covalent geometry : angle 0.71672 / 0.36 ( 4544) SS BOND : bond 0.00231 / 0.12 ( 7) SS BOND : angle 2.16615 / 1.27 ( 14) hydrogen bonds : bond 0.03443 / 2.26 ( 114) hydrogen bonds : angle 6.27094 / 4.41 ( 285) link_BETA1-4 : bond 0.00318 / 0.16 ( 2) link_BETA1-4 : angle 0.84351 / 0.62 ( 6) link_NAG-ASN : bond 0.00002 / 0.00 ( 1) link_NAG-ASN : angle 1.56404 / 0.91 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 739.20 seconds wall clock time: 13 minutes 21.20 seconds (801.20 seconds total)