Starting phenix.real_space_refine on Thu Jul 2 07:17:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nll_12465/07_2026/7nll_12465.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nll_12465/07_2026/7nll_12465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nll_12465/07_2026/7nll_12465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nll_12465/07_2026/7nll_12465.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nll_12465/07_2026/7nll_12465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nll_12465/07_2026/7nll_12465.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7nll_12465/07_2026/7nll_12465.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nll_12465/07_2026/7nll_12465.cif" } resolution = 2.89 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 ------------------------------------------------------------------------------- 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= 0.078 sd= 0.125 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 2915 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 22 5.16 5 C 3220 2.51 5 N 829 2.21 5 O 985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 5056 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1501 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 184} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1494 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 183} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1021 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "C" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1012 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'RTV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'RTV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.14, per 1000 atoms: 0.23 Number of scatterers: 5056 At special positions: 0 Unit cell: (92.92, 57.57, 105.04, 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 22 16.00 O 985 8.00 N 829 7.00 C 3220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 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 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " 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 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 133.1 milliseconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 10 sheets defined 15.2% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.597A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.330A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.330A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN B 409 " --> 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 helix chain 'D' and resid 337 through 343 removed outlier: 3.597A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 383 through 388 removed outlier: 4.329A pdb=" N ASN D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.329A pdb=" N ARG D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN D 409 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 114 through 118 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.614A pdb=" N TYR C 109 " --> pdb=" O CYS B 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'A' and resid 11 through 12 removed outlier: 6.753A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.753A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 417 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: 0.58 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1620 1.34 - 1.46: 1413 1.46 - 1.58: 2139 1.58 - 1.70: 0 1.70 - 1.81: 24 Bond restraints: 5196 Sorted by residual: bond pdb=" C5 RTV D1001 " pdb=" O5 RTV D1001 " ideal model delta sigma weight residual 1.411 1.436 -0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" C5 RTV B1001 " pdb=" O5 RTV B1001 " ideal model delta sigma weight residual 1.411 1.435 -0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" C1 RTV B1001 " pdb=" O5 RTV B1001 " ideal model delta sigma weight residual 1.406 1.428 -0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C2 RTV B1001 " pdb=" C3 RTV B1001 " ideal model delta sigma weight residual 1.547 1.525 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C4 RTV B1001 " pdb=" C5 RTV B1001 " ideal model delta sigma weight residual 1.547 1.526 0.021 2.00e-02 2.50e+03 1.12e+00 ... (remaining 5191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 6519 0.88 - 1.77: 434 1.77 - 2.65: 85 2.65 - 3.53: 36 3.53 - 4.42: 8 Bond angle restraints: 7082 Sorted by residual: angle pdb=" N TYR C 109 " pdb=" CA TYR C 109 " pdb=" C TYR C 109 " ideal model delta sigma weight residual 108.34 105.46 2.88 1.64e+00 3.72e-01 3.09e+00 angle pdb=" N TYR A 109 " pdb=" CA TYR A 109 " pdb=" C TYR A 109 " ideal model delta sigma weight residual 108.34 105.46 2.88 1.64e+00 3.72e-01 3.08e+00 angle pdb=" CA TYR B 369 " pdb=" CB TYR B 369 " pdb=" CG TYR B 369 " ideal model delta sigma weight residual 113.90 116.98 -3.08 1.80e+00 3.09e-01 2.93e+00 angle pdb=" CA TYR D 369 " pdb=" CB TYR D 369 " pdb=" CG TYR D 369 " ideal model delta sigma weight residual 113.90 116.95 -3.05 1.80e+00 3.09e-01 2.87e+00 angle pdb=" N ASP A 119 " pdb=" CA ASP A 119 " pdb=" C ASP A 119 " ideal model delta sigma weight residual 111.36 113.10 -1.74 1.09e+00 8.42e-01 2.54e+00 ... (remaining 7077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 2749 15.77 - 31.54: 194 31.54 - 47.30: 37 47.30 - 63.07: 6 63.07 - 78.84: 2 Dihedral angle restraints: 2988 sinusoidal: 1100 harmonic: 1888 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.00 36.00 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.02 35.98 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CA ARG D 408 " pdb=" CB ARG D 408 " pdb=" CG ARG D 408 " pdb=" CD ARG D 408 " ideal model delta sinusoidal sigma weight residual -180.00 -131.61 -48.39 3 1.50e+01 4.44e-03 8.63e+00 ... (remaining 2985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.000: 745 1.000 - 2.000: 0 2.000 - 3.001: 0 3.001 - 4.001: 0 4.001 - 5.001: 2 Chirality restraints: 747 Sorted by residual: chirality pdb=" C2 RTV D1001 " pdb=" C1 RTV D1001 " pdb=" C3 RTV D1001 " pdb=" N2 RTV D1001 " both_signs ideal model delta sigma weight residual False 2.50 -2.50 5.00 2.00e-01 2.50e+01 6.25e+02 chirality pdb=" C2 RTV B1001 " pdb=" C1 RTV B1001 " pdb=" C3 RTV B1001 " pdb=" N2 RTV B1001 " both_signs ideal model delta sigma weight residual False 2.50 -2.50 5.00 2.00e-01 2.50e+01 6.25e+02 chirality pdb=" CA ILE A 51 " pdb=" N ILE A 51 " pdb=" C ILE A 51 " pdb=" CB ILE A 51 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 744 not shown) Planarity restraints: 927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 116 " 0.010 2.00e-02 2.50e+03 7.11e-03 1.27e+00 pdb=" CG TRP C 116 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP C 116 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP C 116 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 116 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 116 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 116 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 116 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 116 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 116 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 116 " -0.010 2.00e-02 2.50e+03 6.98e-03 1.22e+00 pdb=" CG TRP A 116 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 116 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 116 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 116 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 116 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 116 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 116 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 109 " -0.006 2.00e-02 2.50e+03 6.69e-03 8.94e-01 pdb=" CG TYR C 109 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 109 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 109 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 109 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 109 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 109 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 109 " 0.001 2.00e-02 2.50e+03 ... (remaining 924 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 1059 2.78 - 3.31: 4439 3.31 - 3.84: 8558 3.84 - 4.37: 10483 4.37 - 4.90: 17832 Nonbonded interactions: 42371 Sorted by model distance: nonbonded pdb=" ND2 ASN B 343 " pdb=" O7 RTV B1001 " model vdw 2.255 3.120 nonbonded pdb=" N GLY C 15 " pdb=" O LEU C 86 " model vdw 2.557 3.120 nonbonded pdb=" N GLY A 15 " pdb=" O LEU A 86 " model vdw 2.557 3.120 nonbonded pdb=" N GLN C 13 " pdb=" OE1 GLN C 13 " model vdw 2.571 3.120 nonbonded pdb=" N GLN A 13 " pdb=" OE1 GLN A 13 " model vdw 2.572 3.120 ... (remaining 42366 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' and resid 2 through 133) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 333 through 381 or (resid 382 and (name N or name CA or na \ me C or name O or name CB )) or resid 383 through 527 or resid 1001)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.020 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 5.130 Find NCS groups from input model: 0.110 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.003 0.028 5206 Z= 0.121 Angle : 0.550 4.419 7102 Z= 0.304 Chirality : 0.263 5.001 747 Planarity : 0.004 0.023 927 Dihedral : 10.855 78.842 1774 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.34 (0.31), residues: 648 helix: -0.59 (0.84), residues: 36 sheet: 2.74 (0.37), residues: 164 loop : 0.35 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.016 0.001 TYR C 109 PHE 0.012 0.001 PHE B 347 TRP 0.019 0.002 TRP C 116 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 5196) covalent geometry : angle 0.54912 / 0.30 ( 7082) SS BOND : bond 0.00204 / 0.13 ( 10) SS BOND : angle 0.71170 / 0.48 ( 20) hydrogen bonds : bond 0.23601 / 15.92 ( 171) hydrogen bonds : angle 9.26000 / 6.78 ( 417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8321 (m-30) cc_final: 0.8049 (m-30) REVERT: B 483 VAL cc_start: 0.8283 (t) cc_final: 0.8058 (m) REVERT: D 493 GLN cc_start: 0.8064 (tp40) cc_final: 0.7739 (tp40) REVERT: A 73 ASP cc_start: 0.8075 (t0) cc_final: 0.7862 (t0) REVERT: C 32 TYR cc_start: 0.9068 (m-80) cc_final: 0.8780 (m-80) REVERT: C 86 LEU cc_start: 0.8191 (mt) cc_final: 0.7976 (mt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.3904 time to fit residues: 66.6815 Evaluate side-chains 116 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 30.0000 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 20.0000 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 ASN A 74 ASN C 39 GLN C 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.102847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087619 restraints weight = 8570.727| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.73 r_work: 0.3161 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5206 Z= 0.129 Angle : 0.538 4.855 7102 Z= 0.291 Chirality : 0.044 0.173 747 Planarity : 0.004 0.037 927 Dihedral : 4.017 12.950 730 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.87 % Allowed : 14.18 % Favored : 82.95 % 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: 1.11 (0.31), residues: 648 helix: -0.71 (0.82), residues: 38 sheet: 2.57 (0.37), residues: 166 loop : 0.18 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.019 0.001 TYR B 369 PHE 0.010 0.001 PHE C 68 TRP 0.011 0.001 TRP C 116 HIS 0.000 0.000 HIS D 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 5196) covalent geometry : angle 0.53506 / 0.29 ( 7082) SS BOND : bond 0.00332 / 0.26 ( 10) SS BOND : angle 1.24663 / 0.95 ( 20) hydrogen bonds : bond 0.04019 / 2.61 ( 171) hydrogen bonds : angle 7.00369 / 5.14 ( 417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: B 417 LYS cc_start: 0.8286 (ttmm) cc_final: 0.8072 (ttmt) REVERT: B 418 ILE cc_start: 0.8166 (mp) cc_final: 0.7925 (mm) REVERT: B 420 ASP cc_start: 0.8731 (m-30) cc_final: 0.8458 (m-30) REVERT: B 465 GLU cc_start: 0.8913 (tt0) cc_final: 0.8478 (tt0) REVERT: B 498 GLN cc_start: 0.8597 (mm110) cc_final: 0.8388 (tp40) REVERT: D 420 ASP cc_start: 0.8753 (m-30) cc_final: 0.8470 (m-30) REVERT: D 493 GLN cc_start: 0.8368 (tp40) cc_final: 0.8022 (tp40) REVERT: D 498 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8137 (mp10) REVERT: A 6 GLU cc_start: 0.7460 (mp0) cc_final: 0.7182 (mp0) REVERT: A 31 ASP cc_start: 0.8207 (t0) cc_final: 0.7933 (t0) REVERT: A 46 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7797 (pt0) REVERT: A 73 ASP cc_start: 0.8083 (t0) cc_final: 0.7797 (t0) REVERT: C 32 TYR cc_start: 0.9131 (m-80) cc_final: 0.8818 (m-80) REVERT: C 90 ASP cc_start: 0.7908 (m-30) cc_final: 0.7663 (m-30) REVERT: C 95 TYR cc_start: 0.9322 (m-80) cc_final: 0.8947 (m-80) outliers start: 15 outliers final: 5 residues processed: 137 average time/residue: 0.3346 time to fit residues: 48.4823 Evaluate side-chains 126 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 51 optimal weight: 30.0000 chunk 3 optimal weight: 30.0000 chunk 9 optimal weight: 40.0000 chunk 23 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 487 ASN A 74 ASN A 82 GLN C 3 GLN C 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.082956 restraints weight = 8767.342| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.80 r_work: 0.3014 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 5206 Z= 0.246 Angle : 0.613 5.927 7102 Z= 0.326 Chirality : 0.046 0.153 747 Planarity : 0.005 0.036 927 Dihedral : 4.504 16.139 730 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.79 % Allowed : 15.52 % Favored : 79.69 % 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: 0.48 (0.31), residues: 648 helix: -1.12 (0.77), residues: 37 sheet: 1.61 (0.36), residues: 186 loop : -0.12 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 19 TYR 0.019 0.002 TYR B 495 PHE 0.012 0.002 PHE A 68 TRP 0.009 0.002 TRP A 121 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.25 ( 5196) covalent geometry : angle 0.60924 / 0.32 ( 7082) SS BOND : bond 0.00347 / 0.26 ( 10) SS BOND : angle 1.39722 / 1.02 ( 20) hydrogen bonds : bond 0.04283 / 2.79 ( 171) hydrogen bonds : angle 6.89665 / 5.05 ( 417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: B 418 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8164 (mm) REVERT: B 420 ASP cc_start: 0.8883 (m-30) cc_final: 0.8575 (m-30) REVERT: B 493 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: D 420 ASP cc_start: 0.8982 (m-30) cc_final: 0.8754 (m-30) REVERT: D 493 GLN cc_start: 0.8600 (tp40) cc_final: 0.8302 (tp40) REVERT: D 498 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8400 (mp10) REVERT: A 6 GLU cc_start: 0.8180 (mp0) cc_final: 0.7643 (mp0) REVERT: A 46 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8279 (pt0) REVERT: A 73 ASP cc_start: 0.8271 (t0) cc_final: 0.7982 (t0) REVERT: A 103 SER cc_start: 0.8692 (m) cc_final: 0.8435 (p) REVERT: A 108 THR cc_start: 0.9435 (m) cc_final: 0.9156 (p) REVERT: A 128 THR cc_start: 0.8812 (m) cc_final: 0.8575 (p) REVERT: C 32 TYR cc_start: 0.9235 (m-80) cc_final: 0.8885 (m-80) REVERT: C 46 GLU cc_start: 0.8576 (pt0) cc_final: 0.8363 (pt0) REVERT: C 84 ASN cc_start: 0.8725 (m-40) cc_final: 0.8522 (m-40) REVERT: C 90 ASP cc_start: 0.8166 (m-30) cc_final: 0.7815 (m-30) REVERT: C 95 TYR cc_start: 0.9349 (m-80) cc_final: 0.8952 (m-80) outliers start: 25 outliers final: 10 residues processed: 136 average time/residue: 0.3341 time to fit residues: 48.1069 Evaluate side-chains 123 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 63 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 14 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 501 ASN D 487 ASN A 74 ASN C 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.098382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.082854 restraints weight = 8731.900| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.83 r_work: 0.3015 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 5206 Z= 0.186 Angle : 0.573 8.384 7102 Z= 0.302 Chirality : 0.044 0.139 747 Planarity : 0.004 0.034 927 Dihedral : 4.393 15.303 730 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.79 % Allowed : 18.39 % Favored : 76.82 % 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: 0.15 (0.31), residues: 648 helix: -1.42 (0.83), residues: 32 sheet: 1.24 (0.37), residues: 187 loop : -0.29 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 457 TYR 0.016 0.001 TYR B 495 PHE 0.010 0.001 PHE A 68 TRP 0.009 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 5196) covalent geometry : angle 0.57076 / 0.30 ( 7082) SS BOND : bond 0.00291 / 0.22 ( 10) SS BOND : angle 1.13874 / 0.81 ( 20) hydrogen bonds : bond 0.03741 / 2.42 ( 171) hydrogen bonds : angle 6.62359 / 4.80 ( 417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: D 420 ASP cc_start: 0.8942 (m-30) cc_final: 0.8614 (m-30) REVERT: D 493 GLN cc_start: 0.8627 (tp40) cc_final: 0.8318 (tp40) REVERT: D 498 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8395 (mp10) REVERT: A 6 GLU cc_start: 0.8270 (mp0) cc_final: 0.7816 (mp0) REVERT: A 46 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8352 (pt0) REVERT: A 76 LYS cc_start: 0.8223 (mtpm) cc_final: 0.8000 (mtmm) REVERT: A 103 SER cc_start: 0.8830 (m) cc_final: 0.8550 (p) REVERT: C 32 TYR cc_start: 0.9221 (m-80) cc_final: 0.8928 (m-80) REVERT: C 90 ASP cc_start: 0.8209 (m-30) cc_final: 0.7836 (m-30) REVERT: C 95 TYR cc_start: 0.9366 (m-80) cc_final: 0.8922 (m-80) outliers start: 25 outliers final: 15 residues processed: 128 average time/residue: 0.3117 time to fit residues: 42.3473 Evaluate side-chains 124 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.099728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.084330 restraints weight = 8793.719| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.81 r_work: 0.3039 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5206 Z= 0.136 Angle : 0.537 9.391 7102 Z= 0.281 Chirality : 0.043 0.138 747 Planarity : 0.004 0.033 927 Dihedral : 4.175 14.611 730 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.98 % Allowed : 19.35 % Favored : 75.67 % 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: 0.05 (0.31), residues: 648 helix: -1.28 (1.00), residues: 26 sheet: 1.11 (0.37), residues: 187 loop : -0.36 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.016 0.001 TYR B 369 PHE 0.020 0.001 PHE D 486 TRP 0.009 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 5196) covalent geometry : angle 0.53582 / 0.28 ( 7082) SS BOND : bond 0.00303 / 0.19 ( 10) SS BOND : angle 0.85567 / 0.57 ( 20) hydrogen bonds : bond 0.03348 / 2.16 ( 171) hydrogen bonds : angle 6.34309 / 4.57 ( 417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8806 (m-30) cc_final: 0.8547 (m-30) REVERT: B 493 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: D 420 ASP cc_start: 0.8923 (m-30) cc_final: 0.8607 (m-30) REVERT: D 493 GLN cc_start: 0.8642 (tp40) cc_final: 0.8357 (tp40) REVERT: D 498 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8349 (mp10) REVERT: A 6 GLU cc_start: 0.8280 (mp0) cc_final: 0.7754 (mp0) REVERT: A 46 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: A 89 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: A 103 SER cc_start: 0.8869 (m) cc_final: 0.8668 (p) REVERT: C 32 TYR cc_start: 0.9202 (m-80) cc_final: 0.8937 (m-80) REVERT: C 90 ASP cc_start: 0.8266 (m-30) cc_final: 0.7892 (m-30) REVERT: C 95 TYR cc_start: 0.9370 (m-80) cc_final: 0.8995 (m-80) outliers start: 26 outliers final: 16 residues processed: 128 average time/residue: 0.3508 time to fit residues: 47.5023 Evaluate side-chains 130 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 31 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 409 GLN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.081859 restraints weight = 8920.589| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.84 r_work: 0.2992 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 5206 Z= 0.198 Angle : 0.572 10.716 7102 Z= 0.301 Chirality : 0.044 0.140 747 Planarity : 0.004 0.035 927 Dihedral : 4.366 15.886 730 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 6.13 % Allowed : 19.35 % Favored : 74.52 % 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: -0.10 (0.31), residues: 648 helix: -1.44 (0.82), residues: 32 sheet: 0.88 (0.36), residues: 187 loop : -0.38 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 457 TYR 0.016 0.001 TYR B 369 PHE 0.011 0.001 PHE A 68 TRP 0.007 0.001 TRP D 436 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 ( 5196) covalent geometry : angle 0.56989 / 0.30 ( 7082) SS BOND : bond 0.00353 / 0.26 ( 10) SS BOND : angle 1.05927 / 0.73 ( 20) hydrogen bonds : bond 0.03565 / 2.31 ( 171) hydrogen bonds : angle 6.50345 / 4.69 ( 417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8817 (m-30) cc_final: 0.8540 (m-30) REVERT: B 493 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: D 420 ASP cc_start: 0.8933 (m-30) cc_final: 0.8641 (m-30) REVERT: D 493 GLN cc_start: 0.8634 (tp40) cc_final: 0.8368 (tp40) REVERT: D 498 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8425 (mp10) REVERT: A 6 GLU cc_start: 0.8411 (mp0) cc_final: 0.7888 (mp0) REVERT: A 46 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8409 (pt0) REVERT: A 76 LYS cc_start: 0.8304 (mtmm) cc_final: 0.8032 (ptpp) REVERT: A 89 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: C 32 TYR cc_start: 0.9231 (m-80) cc_final: 0.8959 (m-80) REVERT: C 46 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: C 90 ASP cc_start: 0.8301 (m-30) cc_final: 0.7873 (m-30) REVERT: C 95 TYR cc_start: 0.9364 (m-80) cc_final: 0.9023 (m-80) outliers start: 32 outliers final: 21 residues processed: 128 average time/residue: 0.2895 time to fit residues: 39.3055 Evaluate side-chains 133 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 38 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.082199 restraints weight = 8694.849| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.80 r_work: 0.2996 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 5206 Z= 0.205 Angle : 0.581 12.042 7102 Z= 0.302 Chirality : 0.044 0.139 747 Planarity : 0.004 0.038 927 Dihedral : 4.391 15.679 730 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 6.70 % Allowed : 20.31 % Favored : 72.99 % 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: -0.26 (0.31), residues: 648 helix: -1.54 (0.95), residues: 26 sheet: 0.66 (0.36), residues: 187 loop : -0.45 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 457 TYR 0.015 0.001 TYR B 369 PHE 0.010 0.001 PHE A 68 TRP 0.008 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 5196) covalent geometry : angle 0.57948 / 0.30 ( 7082) SS BOND : bond 0.00327 / 0.24 ( 10) SS BOND : angle 1.02953 / 0.70 ( 20) hydrogen bonds : bond 0.03522 / 2.27 ( 171) hydrogen bonds : angle 6.52843 / 4.70 ( 417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8808 (m-30) cc_final: 0.8477 (m-30) REVERT: B 457 ARG cc_start: 0.9139 (ttt90) cc_final: 0.8905 (ttt90) REVERT: B 493 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: D 420 ASP cc_start: 0.8895 (m-30) cc_final: 0.8571 (m-30) REVERT: D 493 GLN cc_start: 0.8625 (tp40) cc_final: 0.8362 (tp40) REVERT: D 498 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8393 (mp10) REVERT: D 517 LEU cc_start: 0.8139 (tp) cc_final: 0.7917 (tt) REVERT: A 6 GLU cc_start: 0.8405 (mp0) cc_final: 0.7816 (mp0) REVERT: A 31 ASP cc_start: 0.8394 (t0) cc_final: 0.8029 (t0) REVERT: A 45 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7792 (mtt180) REVERT: A 46 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8398 (pt0) REVERT: A 89 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8300 (mp0) REVERT: C 32 TYR cc_start: 0.9225 (m-80) cc_final: 0.8943 (m-80) REVERT: C 46 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8297 (pt0) REVERT: C 90 ASP cc_start: 0.8279 (m-30) cc_final: 0.7899 (m-30) REVERT: C 95 TYR cc_start: 0.9354 (m-80) cc_final: 0.9029 (m-80) outliers start: 35 outliers final: 20 residues processed: 126 average time/residue: 0.3116 time to fit residues: 41.6591 Evaluate side-chains 135 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 61 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.083051 restraints weight = 8702.081| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.80 r_work: 0.3014 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5206 Z= 0.161 Angle : 0.591 15.890 7102 Z= 0.296 Chirality : 0.043 0.138 747 Planarity : 0.004 0.037 927 Dihedral : 4.266 15.166 730 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.75 % Allowed : 21.46 % Favored : 72.80 % 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: -0.28 (0.31), residues: 648 helix: -1.28 (0.99), residues: 25 sheet: 0.65 (0.36), residues: 187 loop : -0.49 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.015 0.001 TYR B 369 PHE 0.007 0.001 PHE A 68 TRP 0.008 0.001 TRP D 436 HIS 0.000 0.000 HIS D 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 5196) covalent geometry : angle 0.59009 / 0.30 ( 7082) SS BOND : bond 0.00277 / 0.20 ( 10) SS BOND : angle 0.89296 / 0.57 ( 20) hydrogen bonds : bond 0.03296 / 2.13 ( 171) hydrogen bonds : angle 6.37297 / 4.58 ( 417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8793 (m-30) cc_final: 0.8515 (m-30) REVERT: B 493 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7617 (tm-30) REVERT: B 498 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8581 (mp10) REVERT: D 420 ASP cc_start: 0.8888 (m-30) cc_final: 0.8578 (m-30) REVERT: D 493 GLN cc_start: 0.8634 (tp40) cc_final: 0.8375 (tp40) REVERT: D 498 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8351 (mp10) REVERT: D 517 LEU cc_start: 0.8111 (tp) cc_final: 0.7907 (tt) REVERT: A 6 GLU cc_start: 0.7982 (mp0) cc_final: 0.7580 (mp0) REVERT: A 31 ASP cc_start: 0.8293 (t0) cc_final: 0.7836 (t0) REVERT: A 45 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7765 (mtt180) REVERT: A 46 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8392 (pt0) REVERT: A 76 LYS cc_start: 0.8329 (mtmm) cc_final: 0.7961 (ptpp) REVERT: A 89 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8343 (mp0) REVERT: C 32 TYR cc_start: 0.9219 (m-80) cc_final: 0.8951 (m-80) REVERT: C 46 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8285 (pt0) REVERT: C 90 ASP cc_start: 0.8313 (m-30) cc_final: 0.7901 (m-30) REVERT: C 95 TYR cc_start: 0.9357 (m-80) cc_final: 0.9042 (m-80) outliers start: 30 outliers final: 23 residues processed: 125 average time/residue: 0.2838 time to fit residues: 37.6104 Evaluate side-chains 139 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 14 optimal weight: 0.0770 chunk 19 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.099170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.083753 restraints weight = 8650.689| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.79 r_work: 0.3021 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5206 Z= 0.142 Angle : 0.566 13.269 7102 Z= 0.289 Chirality : 0.043 0.136 747 Planarity : 0.004 0.036 927 Dihedral : 4.183 14.876 730 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.17 % Allowed : 22.41 % Favored : 72.41 % 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: -0.34 (0.31), residues: 648 helix: -1.21 (1.01), residues: 25 sheet: 0.62 (0.36), residues: 187 loop : -0.54 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.016 0.001 TYR B 369 PHE 0.006 0.001 PHE A 68 TRP 0.009 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 5196) covalent geometry : angle 0.56514 / 0.29 ( 7082) SS BOND : bond 0.00249 / 0.18 ( 10) SS BOND : angle 0.84880 / 0.53 ( 20) hydrogen bonds : bond 0.03204 / 2.07 ( 171) hydrogen bonds : angle 6.31480 / 4.55 ( 417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 408 ARG cc_start: 0.9135 (tmm160) cc_final: 0.8820 (ptm-80) REVERT: B 493 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: D 420 ASP cc_start: 0.8856 (m-30) cc_final: 0.8534 (m-30) REVERT: D 493 GLN cc_start: 0.8614 (tp40) cc_final: 0.8355 (tp40) REVERT: D 498 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8314 (mp10) REVERT: D 517 LEU cc_start: 0.8114 (tp) cc_final: 0.7909 (tt) REVERT: A 6 GLU cc_start: 0.8043 (mp0) cc_final: 0.7592 (mp0) REVERT: A 31 ASP cc_start: 0.8297 (t0) cc_final: 0.7826 (t0) REVERT: A 45 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7751 (mtt180) REVERT: A 46 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8398 (pt0) REVERT: A 76 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7927 (ptpp) REVERT: A 89 GLU cc_start: 0.8569 (mp0) cc_final: 0.8350 (mp0) REVERT: C 32 TYR cc_start: 0.9219 (m-80) cc_final: 0.8961 (m-80) REVERT: C 46 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: C 90 ASP cc_start: 0.8304 (m-30) cc_final: 0.7860 (m-30) REVERT: C 95 TYR cc_start: 0.9364 (m-80) cc_final: 0.9063 (m-80) outliers start: 27 outliers final: 18 residues processed: 121 average time/residue: 0.3098 time to fit residues: 39.8794 Evaluate side-chains 130 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.098288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.082816 restraints weight = 8705.701| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.79 r_work: 0.3005 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5206 Z= 0.175 Angle : 0.576 10.479 7102 Z= 0.299 Chirality : 0.043 0.138 747 Planarity : 0.004 0.035 927 Dihedral : 4.270 15.370 730 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.60 % Allowed : 22.61 % Favored : 72.80 % 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: -0.39 (0.31), residues: 648 helix: -1.23 (1.03), residues: 25 sheet: 0.55 (0.36), residues: 187 loop : -0.56 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 457 TYR 0.015 0.001 TYR B 369 PHE 0.008 0.001 PHE A 68 TRP 0.008 0.001 TRP D 436 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 5196) covalent geometry : angle 0.57431 / 0.30 ( 7082) SS BOND : bond 0.00290 / 0.21 ( 10) SS BOND : angle 0.95433 / 0.62 ( 20) hydrogen bonds : bond 0.03377 / 2.18 ( 171) hydrogen bonds : angle 6.36185 / 4.57 ( 417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 408 ARG cc_start: 0.9110 (tmm160) cc_final: 0.8652 (ppt170) REVERT: B 493 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: D 420 ASP cc_start: 0.8868 (m-30) cc_final: 0.8634 (m-30) REVERT: D 493 GLN cc_start: 0.8627 (tp40) cc_final: 0.8364 (tp40) REVERT: D 498 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8346 (mp10) REVERT: A 6 GLU cc_start: 0.8075 (mp0) cc_final: 0.7658 (mp0) REVERT: A 31 ASP cc_start: 0.8295 (t0) cc_final: 0.7811 (t0) REVERT: A 45 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7769 (mtt180) REVERT: A 46 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8412 (pt0) REVERT: A 89 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: C 32 TYR cc_start: 0.9221 (m-80) cc_final: 0.8948 (m-80) REVERT: C 46 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: C 90 ASP cc_start: 0.8324 (m-30) cc_final: 0.7898 (m-30) REVERT: C 95 TYR cc_start: 0.9363 (m-80) cc_final: 0.9071 (m-80) outliers start: 24 outliers final: 19 residues processed: 120 average time/residue: 0.3034 time to fit residues: 38.6082 Evaluate side-chains 131 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 43 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 42 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN C 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.098261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.083064 restraints weight = 8769.441| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.77 r_work: 0.3013 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5206 Z= 0.161 Angle : 0.584 12.194 7102 Z= 0.298 Chirality : 0.043 0.136 747 Planarity : 0.004 0.035 927 Dihedral : 4.242 15.219 730 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.98 % Allowed : 22.22 % Favored : 72.80 % 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: -0.40 (0.31), residues: 648 helix: -1.22 (1.02), residues: 25 sheet: 0.53 (0.36), residues: 187 loop : -0.57 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.015 0.001 TYR B 369 PHE 0.009 0.001 PHE D 486 TRP 0.008 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 5196) covalent geometry : angle 0.58260 / 0.30 ( 7082) SS BOND : bond 0.00269 / 0.20 ( 10) SS BOND : angle 0.90239 / 0.58 ( 20) hydrogen bonds : bond 0.03289 / 2.12 ( 171) hydrogen bonds : angle 6.35872 / 4.57 ( 417) =============================================================================== Job complete usr+sys time: 1598.43 seconds wall clock time: 27 minutes 53.75 seconds (1673.75 seconds total)