Starting phenix.real_space_refine on Tue Feb 3 16:10:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zb0_39893/02_2026/8zb0_39893.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zb0_39893/02_2026/8zb0_39893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zb0_39893/02_2026/8zb0_39893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zb0_39893/02_2026/8zb0_39893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zb0_39893/02_2026/8zb0_39893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zb0_39893/02_2026/8zb0_39893.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 46 5.16 5 C 3136 2.51 5 N 822 2.21 5 O 868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4880 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2436 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2381 SG CYS A 433 25.072 34.918 24.201 1.00 44.13 S Restraints were copied for chains: B Time building chain proxies: 1.54, per 1000 atoms: 0.32 Number of scatterers: 4880 At special positions: 0 Unit cell: (69.966, 57.798, 125.736, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 46 16.00 O 868 8.00 N 822 7.00 C 3136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 311 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS B 291 " distance=2.08 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 311 " distance=2.02 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 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 295.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" ND1 HIS A 408 " pdb="ZN ZN A 603 " - pdb=" SG CYS B 437 " pdb="ZN ZN A 603 " - pdb=" ND1 HIS A 413 " pdb=" ZN A 604 " pdb="ZN ZN A 604 " - pdb=" SG CYS A 433 " pdb="ZN ZN A 604 " - pdb=" ND1 HIS A 387 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 408 " pdb="ZN ZN B 603 " - pdb=" SG CYS A 437 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 413 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 433 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 387 " 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1240 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 55.8% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.089A pdb=" N LEU A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.621A pdb=" N SER A 46 " --> pdb=" O HIS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.694A pdb=" N ALA A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 106 removed outlier: 3.642A pdb=" N GLY A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 133 Processing helix chain 'A' and resid 243 through 268 removed outlier: 4.138A pdb=" N HIS A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP A 255 " --> pdb=" O HIS A 251 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 317 through 344 removed outlier: 3.877A pdb=" N TYR A 330 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 352 through 363 removed outlier: 3.543A pdb=" N VAL A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 409 removed outlier: 3.737A pdb=" N VAL A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 32 Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.622A pdb=" N SER B 46 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 57 removed outlier: 3.694A pdb=" N ALA B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 106 removed outlier: 3.642A pdb=" N GLY B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 133 Processing helix chain 'B' and resid 243 through 268 removed outlier: 4.138A pdb=" N HIS B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP B 255 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 Processing helix chain 'B' and resid 317 through 344 removed outlier: 3.877A pdb=" N TYR B 330 " --> pdb=" O CYS B 326 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 352 through 363 removed outlier: 3.542A pdb=" N VAL B 363 " --> pdb=" O GLU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 409 removed outlier: 3.737A pdb=" N VAL B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 374 through 376 removed outlier: 3.632A pdb=" N TRP A 375 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 383 " --> pdb=" O TRP A 375 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 414 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 374 through 376 removed outlier: 3.632A pdb=" N TRP B 375 " --> pdb=" O ILE B 383 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 383 " --> pdb=" O TRP B 375 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 414 " --> pdb=" O ILE B 382 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 780 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: 0.72 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1447 1.33 - 1.45: 722 1.45 - 1.57: 2721 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 4956 Sorted by residual: bond pdb=" N VAL A 313 " pdb=" CA VAL A 313 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.07e-02 8.73e+03 1.14e+01 bond pdb=" N VAL B 313 " pdb=" CA VAL B 313 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.07e-02 8.73e+03 1.13e+01 bond pdb=" N HIS B 65 " pdb=" CA HIS B 65 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.25e-02 6.40e+03 7.16e+00 bond pdb=" N GLN B 440 " pdb=" CA GLN B 440 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.34e-02 5.57e+03 7.14e+00 bond pdb=" N GLN A 440 " pdb=" CA GLN A 440 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.34e-02 5.57e+03 7.03e+00 ... (remaining 4951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 6269 2.08 - 4.17: 413 4.17 - 6.25: 47 6.25 - 8.33: 15 8.33 - 10.42: 4 Bond angle restraints: 6748 Sorted by residual: angle pdb=" C ASP B 289 " pdb=" N PRO B 290 " pdb=" CA PRO B 290 " ideal model delta sigma weight residual 119.05 127.32 -8.27 1.11e+00 8.12e-01 5.55e+01 angle pdb=" C ASP A 289 " pdb=" N PRO A 290 " pdb=" CA PRO A 290 " ideal model delta sigma weight residual 119.05 127.31 -8.26 1.11e+00 8.12e-01 5.54e+01 angle pdb=" N PRO A 290 " pdb=" CA PRO A 290 " pdb=" C PRO A 290 " ideal model delta sigma weight residual 113.53 120.63 -7.10 1.39e+00 5.18e-01 2.61e+01 angle pdb=" N GLU B 58 " pdb=" CA GLU B 58 " pdb=" C GLU B 58 " ideal model delta sigma weight residual 113.88 107.62 6.26 1.23e+00 6.61e-01 2.59e+01 angle pdb=" N PRO B 290 " pdb=" CA PRO B 290 " pdb=" C PRO B 290 " ideal model delta sigma weight residual 113.53 120.60 -7.07 1.39e+00 5.18e-01 2.59e+01 ... (remaining 6743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 2567 17.49 - 34.99: 292 34.99 - 52.48: 74 52.48 - 69.97: 10 69.97 - 87.47: 4 Dihedral angle restraints: 2947 sinusoidal: 1043 harmonic: 1904 Sorted by residual: dihedral pdb=" CB CYS A 286 " pdb=" SG CYS A 286 " pdb=" SG CYS A 311 " pdb=" CB CYS A 311 " ideal model delta sinusoidal sigma weight residual 93.00 173.58 -80.58 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS B 286 " pdb=" SG CYS B 286 " pdb=" SG CYS B 311 " pdb=" CB CYS B 311 " ideal model delta sinusoidal sigma weight residual 93.00 173.57 -80.57 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CD ARG A 59 " pdb=" NE ARG A 59 " pdb=" CZ ARG A 59 " pdb=" NH1 ARG A 59 " ideal model delta sinusoidal sigma weight residual 0.00 -62.80 62.80 1 1.00e+01 1.00e-02 5.21e+01 ... (remaining 2944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 454 0.046 - 0.091: 278 0.091 - 0.137: 77 0.137 - 0.183: 25 0.183 - 0.229: 6 Chirality restraints: 840 Sorted by residual: chirality pdb=" CA ARG B 381 " pdb=" N ARG B 381 " pdb=" C ARG B 381 " pdb=" CB ARG B 381 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ARG A 381 " pdb=" N ARG A 381 " pdb=" C ARG A 381 " pdb=" CB ARG A 381 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ARG B 59 " pdb=" N ARG B 59 " pdb=" C ARG B 59 " pdb=" CB ARG B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 837 not shown) Planarity restraints: 846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 59 " 0.976 9.50e-02 1.11e+02 4.38e-01 1.16e+02 pdb=" NE ARG B 59 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG B 59 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 59 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 59 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 59 " -0.976 9.50e-02 1.11e+02 4.38e-01 1.16e+02 pdb=" NE ARG A 59 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 59 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 59 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 59 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 30 " 0.574 9.50e-02 1.11e+02 2.57e-01 4.04e+01 pdb=" NE ARG B 30 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG B 30 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 30 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 30 " 0.019 2.00e-02 2.50e+03 ... (remaining 843 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 19 2.33 - 2.97: 2688 2.97 - 3.61: 6670 3.61 - 4.26: 9805 4.26 - 4.90: 16492 Nonbonded interactions: 35674 Sorted by model distance: nonbonded pdb=" OE2 GLU B 420 " pdb="ZN ZN B 604 " model vdw 1.682 2.230 nonbonded pdb=" OE2 GLU A 420 " pdb="ZN ZN A 604 " model vdw 1.682 2.230 nonbonded pdb=" OD2 ASP A 255 " pdb="ZN ZN A 602 " model vdw 1.759 2.230 nonbonded pdb=" OD2 ASP B 255 " pdb="ZN ZN B 602 " model vdw 1.759 2.230 nonbonded pdb=" OD2 ASP A 47 " pdb="ZN ZN A 602 " model vdw 1.793 2.230 ... (remaining 35669 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.720 Find NCS groups from input model: 0.040 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 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 : 0.021 0.628 4969 Z= 0.813 Angle : 1.175 10.416 6754 Z= 0.696 Chirality : 0.063 0.229 840 Planarity : 0.025 0.438 846 Dihedral : 15.898 87.467 1698 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.92 % Allowed : 12.00 % Favored : 87.08 % Rotamer: Outliers : 4.78 % Allowed : 16.14 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.98 (0.24), residues: 650 helix: -2.34 (0.21), residues: 378 sheet: -6.06 (0.22), residues: 32 loop : -4.39 (0.27), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 76 TYR 0.010 0.002 TYR A 396 PHE 0.023 0.003 PHE A 21 TRP 0.026 0.004 TRP A 375 HIS 0.005 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.01303 ( 4956) covalent geometry : angle 1.17499 ( 6748) SS BOND : bond 0.02893 ( 3) SS BOND : angle 1.46528 ( 6) hydrogen bonds : bond 0.15082 ( 262) hydrogen bonds : angle 6.76006 ( 780) metal coordination : bond 0.38002 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.178 Fit side-chains REVERT: A 246 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6383 (mmm160) REVERT: A 312 TRP cc_start: 0.5026 (OUTLIER) cc_final: 0.4814 (t60) REVERT: A 391 GLU cc_start: 0.7111 (tp30) cc_final: 0.6719 (pm20) REVERT: B 246 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6340 (mmm160) REVERT: B 312 TRP cc_start: 0.5213 (OUTLIER) cc_final: 0.4865 (t60) REVERT: B 330 TYR cc_start: 0.8649 (t80) cc_final: 0.8430 (t80) REVERT: B 391 GLU cc_start: 0.7164 (tp30) cc_final: 0.6721 (pm20) outliers start: 24 outliers final: 18 residues processed: 88 average time/residue: 0.0736 time to fit residues: 8.1186 Evaluate side-chains 77 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 312 TRP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 441 CYS Chi-restraints excluded: chain B residue 30 ARG Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 246 ARG Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 312 TRP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 441 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.0010 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS A 108 HIS B 65 HIS B 108 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.186611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.159726 restraints weight = 4455.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.159201 restraints weight = 5515.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.159325 restraints weight = 5533.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.159932 restraints weight = 4786.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.159962 restraints weight = 4758.760| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4969 Z= 0.167 Angle : 0.614 6.611 6754 Z= 0.323 Chirality : 0.043 0.133 840 Planarity : 0.004 0.029 846 Dihedral : 9.645 74.070 736 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.69 % Favored : 92.00 % Rotamer: Outliers : 3.19 % Allowed : 19.72 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.31), residues: 650 helix: -0.24 (0.26), residues: 380 sheet: -5.10 (0.52), residues: 42 loop : -3.47 (0.34), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.009 0.001 TYR A 330 PHE 0.011 0.002 PHE A 21 TRP 0.010 0.002 TRP A 375 HIS 0.010 0.002 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 4956) covalent geometry : angle 0.61274 ( 6748) SS BOND : bond 0.00270 ( 3) SS BOND : angle 1.20934 ( 6) hydrogen bonds : bond 0.04910 ( 262) hydrogen bonds : angle 4.10905 ( 780) metal coordination : bond 0.01017 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.155 Fit side-chains REVERT: A 314 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7565 (tt) REVERT: B 314 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7554 (tt) REVERT: B 391 GLU cc_start: 0.6853 (tp30) cc_final: 0.6576 (pm20) outliers start: 16 outliers final: 9 residues processed: 61 average time/residue: 0.0483 time to fit residues: 4.0151 Evaluate side-chains 54 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 65 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 366 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS B 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.186817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.151696 restraints weight = 4453.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.154239 restraints weight = 3617.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155329 restraints weight = 3075.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.155855 restraints weight = 2835.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.157273 restraints weight = 2628.420| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4969 Z= 0.146 Angle : 0.578 6.439 6754 Z= 0.302 Chirality : 0.041 0.128 840 Planarity : 0.003 0.030 846 Dihedral : 5.693 53.091 692 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.78 % Allowed : 21.51 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.59 (0.33), residues: 650 helix: 0.54 (0.28), residues: 378 sheet: -5.60 (0.31), residues: 32 loop : -3.07 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 30 TYR 0.006 0.001 TYR A 396 PHE 0.011 0.001 PHE B 21 TRP 0.010 0.001 TRP A 375 HIS 0.007 0.002 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4956) covalent geometry : angle 0.57760 ( 6748) SS BOND : bond 0.00195 ( 3) SS BOND : angle 1.10977 ( 6) hydrogen bonds : bond 0.04405 ( 262) hydrogen bonds : angle 3.68865 ( 780) metal coordination : bond 0.00222 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.175 Fit side-chains REVERT: A 102 GLU cc_start: 0.6134 (mm-30) cc_final: 0.5861 (mt-10) REVERT: A 314 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7486 (tt) REVERT: B 102 GLU cc_start: 0.6110 (mm-30) cc_final: 0.5774 (mt-10) REVERT: B 314 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7564 (tt) REVERT: B 391 GLU cc_start: 0.6985 (tp30) cc_final: 0.6563 (pm20) outliers start: 19 outliers final: 16 residues processed: 57 average time/residue: 0.0399 time to fit residues: 3.4592 Evaluate side-chains 56 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 65 HIS Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 366 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 61 optimal weight: 0.0050 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 15 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 49 optimal weight: 6.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS B 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.193325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.158180 restraints weight = 4399.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.160570 restraints weight = 3655.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.162257 restraints weight = 3086.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163234 restraints weight = 2735.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163234 restraints weight = 2475.302| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4969 Z= 0.105 Angle : 0.502 5.603 6754 Z= 0.265 Chirality : 0.040 0.119 840 Planarity : 0.003 0.030 846 Dihedral : 5.342 52.205 692 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.78 % Allowed : 20.12 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.35), residues: 650 helix: 1.07 (0.28), residues: 378 sheet: -4.47 (0.62), residues: 42 loop : -2.77 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.004 0.001 TYR A 396 PHE 0.010 0.001 PHE A 21 TRP 0.007 0.001 TRP A 375 HIS 0.006 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 4956) covalent geometry : angle 0.50136 ( 6748) SS BOND : bond 0.00140 ( 3) SS BOND : angle 0.97350 ( 6) hydrogen bonds : bond 0.03611 ( 262) hydrogen bonds : angle 3.30311 ( 780) metal coordination : bond 0.00244 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 44 time to evaluate : 0.107 Fit side-chains REVERT: A 255 ASP cc_start: 0.4992 (OUTLIER) cc_final: 0.4681 (m-30) REVERT: B 255 ASP cc_start: 0.5042 (OUTLIER) cc_final: 0.4781 (m-30) REVERT: B 314 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7546 (tt) REVERT: B 391 GLU cc_start: 0.6932 (tp30) cc_final: 0.6502 (pm20) outliers start: 24 outliers final: 10 residues processed: 66 average time/residue: 0.0534 time to fit residues: 4.8489 Evaluate side-chains 54 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 65 HIS Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 326 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.0870 chunk 50 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 0.4980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.192956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.166607 restraints weight = 4440.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.165134 restraints weight = 6076.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.166015 restraints weight = 6637.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.166424 restraints weight = 4787.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.166526 restraints weight = 4393.425| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4969 Z= 0.119 Angle : 0.510 5.515 6754 Z= 0.267 Chirality : 0.041 0.169 840 Planarity : 0.003 0.028 846 Dihedral : 4.806 52.092 688 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 5.18 % Allowed : 20.32 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.35), residues: 650 helix: 1.29 (0.28), residues: 382 sheet: -4.68 (0.51), residues: 32 loop : -2.62 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.007 0.001 TYR B 330 PHE 0.011 0.001 PHE B 21 TRP 0.010 0.001 TRP A 375 HIS 0.007 0.001 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 4956) covalent geometry : angle 0.50921 ( 6748) SS BOND : bond 0.00156 ( 3) SS BOND : angle 0.85048 ( 6) hydrogen bonds : bond 0.03626 ( 262) hydrogen bonds : angle 3.20283 ( 780) metal coordination : bond 0.00259 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 0.110 Fit side-chains REVERT: A 368 GLU cc_start: 0.7705 (tt0) cc_final: 0.7334 (tt0) REVERT: B 314 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7587 (tt) REVERT: B 368 GLU cc_start: 0.7722 (tt0) cc_final: 0.7364 (tt0) REVERT: B 391 GLU cc_start: 0.6844 (tp30) cc_final: 0.6512 (pm20) outliers start: 26 outliers final: 18 residues processed: 64 average time/residue: 0.0438 time to fit residues: 4.1844 Evaluate side-chains 58 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 65 HIS Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 397 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.194256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.168425 restraints weight = 4427.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.167524 restraints weight = 5823.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.168065 restraints weight = 6332.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.168166 restraints weight = 5397.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.168458 restraints weight = 4676.828| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4969 Z= 0.105 Angle : 0.482 5.147 6754 Z= 0.253 Chirality : 0.040 0.120 840 Planarity : 0.003 0.028 846 Dihedral : 4.708 52.218 688 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.38 % Allowed : 20.92 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.35), residues: 650 helix: 1.76 (0.29), residues: 370 sheet: -4.29 (0.60), residues: 32 loop : -2.44 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.005 0.001 TYR B 330 PHE 0.012 0.001 PHE A 21 TRP 0.009 0.001 TRP A 375 HIS 0.005 0.001 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 4956) covalent geometry : angle 0.48181 ( 6748) SS BOND : bond 0.00143 ( 3) SS BOND : angle 0.78131 ( 6) hydrogen bonds : bond 0.03440 ( 262) hydrogen bonds : angle 3.05192 ( 780) metal coordination : bond 0.00197 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.170 Fit side-chains REVERT: A 368 GLU cc_start: 0.7684 (tt0) cc_final: 0.7285 (tt0) REVERT: B 368 GLU cc_start: 0.7657 (tt0) cc_final: 0.7263 (tt0) REVERT: B 391 GLU cc_start: 0.6859 (tp30) cc_final: 0.6546 (pm20) outliers start: 22 outliers final: 18 residues processed: 64 average time/residue: 0.0376 time to fit residues: 3.6534 Evaluate side-chains 59 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 397 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.184257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.158627 restraints weight = 4478.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156531 restraints weight = 5494.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156850 restraints weight = 5277.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.157530 restraints weight = 4466.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.157524 restraints weight = 3969.057| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4969 Z= 0.204 Angle : 0.601 5.855 6754 Z= 0.313 Chirality : 0.044 0.140 840 Planarity : 0.003 0.028 846 Dihedral : 4.712 29.257 686 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.98 % Allowed : 20.92 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.34), residues: 650 helix: 1.56 (0.28), residues: 368 sheet: -4.16 (0.65), residues: 32 loop : -2.68 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 30 TYR 0.007 0.001 TYR A 396 PHE 0.016 0.001 PHE A 21 TRP 0.015 0.002 TRP A 375 HIS 0.009 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 4956) covalent geometry : angle 0.60046 ( 6748) SS BOND : bond 0.00275 ( 3) SS BOND : angle 0.75236 ( 6) hydrogen bonds : bond 0.04760 ( 262) hydrogen bonds : angle 3.51832 ( 780) metal coordination : bond 0.00342 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 0.180 Fit side-chains REVERT: A 368 GLU cc_start: 0.7571 (tt0) cc_final: 0.7172 (tt0) REVERT: A 391 GLU cc_start: 0.6964 (pm20) cc_final: 0.6647 (tp30) REVERT: B 44 MET cc_start: 0.6501 (ttp) cc_final: 0.6056 (ttt) REVERT: B 368 GLU cc_start: 0.7528 (tt0) cc_final: 0.7170 (tt0) REVERT: B 391 GLU cc_start: 0.6855 (tp30) cc_final: 0.6631 (pm20) outliers start: 25 outliers final: 24 residues processed: 67 average time/residue: 0.0460 time to fit residues: 4.6243 Evaluate side-chains 66 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 406 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.188710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.161837 restraints weight = 4452.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.160537 restraints weight = 5995.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.161008 restraints weight = 5474.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.161242 restraints weight = 4811.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.161502 restraints weight = 4123.248| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4969 Z= 0.144 Angle : 0.531 5.585 6754 Z= 0.278 Chirality : 0.041 0.123 840 Planarity : 0.003 0.029 846 Dihedral : 4.501 28.670 686 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.58 % Allowed : 21.91 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.34), residues: 650 helix: 1.91 (0.27), residues: 368 sheet: -3.99 (0.68), residues: 32 loop : -2.60 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 30 TYR 0.006 0.001 TYR B 396 PHE 0.012 0.001 PHE A 21 TRP 0.011 0.001 TRP B 375 HIS 0.006 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 4956) covalent geometry : angle 0.53076 ( 6748) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.69919 ( 6) hydrogen bonds : bond 0.04033 ( 262) hydrogen bonds : angle 3.24320 ( 780) metal coordination : bond 0.00235 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 40 time to evaluate : 0.119 Fit side-chains REVERT: A 368 GLU cc_start: 0.7584 (tt0) cc_final: 0.7258 (tt0) REVERT: A 391 GLU cc_start: 0.6807 (pm20) cc_final: 0.6510 (tp30) REVERT: B 44 MET cc_start: 0.6175 (ttp) cc_final: 0.5760 (ttt) REVERT: B 368 GLU cc_start: 0.7565 (tt0) cc_final: 0.7260 (tt0) REVERT: B 391 GLU cc_start: 0.6791 (tp30) cc_final: 0.6577 (pm20) outliers start: 23 outliers final: 21 residues processed: 62 average time/residue: 0.0431 time to fit residues: 4.0242 Evaluate side-chains 61 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 40 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain B residue 406 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.190552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.155801 restraints weight = 4418.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.158243 restraints weight = 3494.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.159499 restraints weight = 2975.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160559 restraints weight = 2672.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160844 restraints weight = 2492.703| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4969 Z= 0.116 Angle : 0.498 6.189 6754 Z= 0.260 Chirality : 0.040 0.118 840 Planarity : 0.003 0.029 846 Dihedral : 4.257 27.550 686 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.19 % Allowed : 23.11 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.34), residues: 650 helix: 2.44 (0.27), residues: 362 sheet: -3.73 (0.71), residues: 32 loop : -2.28 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 30 TYR 0.004 0.001 TYR B 396 PHE 0.010 0.001 PHE A 21 TRP 0.009 0.001 TRP B 375 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4956) covalent geometry : angle 0.49764 ( 6748) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.60868 ( 6) hydrogen bonds : bond 0.03517 ( 262) hydrogen bonds : angle 3.01251 ( 780) metal coordination : bond 0.00221 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.192 Fit side-chains REVERT: A 368 GLU cc_start: 0.7585 (tt0) cc_final: 0.7297 (tt0) REVERT: A 391 GLU cc_start: 0.6761 (pm20) cc_final: 0.6491 (tp30) REVERT: B 44 MET cc_start: 0.6121 (ttp) cc_final: 0.5728 (ttt) REVERT: B 368 GLU cc_start: 0.7581 (tt0) cc_final: 0.7305 (tt0) REVERT: B 391 GLU cc_start: 0.6786 (tp30) cc_final: 0.6470 (pm20) outliers start: 16 outliers final: 16 residues processed: 60 average time/residue: 0.0560 time to fit residues: 4.8075 Evaluate side-chains 60 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 397 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.187038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.158932 restraints weight = 4469.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155796 restraints weight = 7568.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.157267 restraints weight = 7108.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.157049 restraints weight = 4842.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157290 restraints weight = 4300.865| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4969 Z= 0.151 Angle : 0.544 8.675 6754 Z= 0.282 Chirality : 0.042 0.123 840 Planarity : 0.003 0.031 846 Dihedral : 4.415 27.819 686 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.98 % Allowed : 22.51 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.34), residues: 650 helix: 2.40 (0.27), residues: 360 sheet: -3.63 (0.70), residues: 32 loop : -2.30 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 30 TYR 0.006 0.001 TYR B 396 PHE 0.011 0.001 PHE A 21 TRP 0.012 0.001 TRP B 375 HIS 0.006 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4956) covalent geometry : angle 0.54361 ( 6748) SS BOND : bond 0.00196 ( 3) SS BOND : angle 0.58077 ( 6) hydrogen bonds : bond 0.04067 ( 262) hydrogen bonds : angle 3.20332 ( 780) metal coordination : bond 0.00245 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1300 Ramachandran restraints generated. 650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.175 Fit side-chains REVERT: A 368 GLU cc_start: 0.7594 (tt0) cc_final: 0.7282 (tt0) REVERT: A 391 GLU cc_start: 0.6853 (pm20) cc_final: 0.6524 (tp30) REVERT: B 44 MET cc_start: 0.6291 (ttp) cc_final: 0.5870 (ttt) REVERT: B 368 GLU cc_start: 0.7597 (tt0) cc_final: 0.7303 (tt0) REVERT: B 391 GLU cc_start: 0.6897 (tp30) cc_final: 0.6509 (pm20) outliers start: 20 outliers final: 20 residues processed: 63 average time/residue: 0.0546 time to fit residues: 4.9248 Evaluate side-chains 64 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 CYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 326 CYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 397 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 48 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 7 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.184824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157362 restraints weight = 4483.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.155979 restraints weight = 6254.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.156267 restraints weight = 6156.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.156600 restraints weight = 5302.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.156815 restraints weight = 4476.995| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4969 Z= 0.179 Angle : 0.581 8.354 6754 Z= 0.300 Chirality : 0.043 0.126 840 Planarity : 0.003 0.030 846 Dihedral : 4.581 28.245 686 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.78 % Allowed : 21.91 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.34), residues: 650 helix: 2.13 (0.27), residues: 368 sheet: -3.64 (0.70), residues: 32 loop : -2.49 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 30 TYR 0.007 0.001 TYR B 396 PHE 0.013 0.001 PHE A 21 TRP 0.013 0.002 TRP B 375 HIS 0.006 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 4956) covalent geometry : angle 0.58135 ( 6748) SS BOND : bond 0.00244 ( 3) SS BOND : angle 0.57360 ( 6) hydrogen bonds : bond 0.04445 ( 262) hydrogen bonds : angle 3.36958 ( 780) metal coordination : bond 0.00311 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 784.31 seconds wall clock time: 14 minutes 13.27 seconds (853.27 seconds total)