Starting phenix.real_space_refine on Tue Mar 3 17:19:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nll_12465/03_2026/7nll_12465.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nll_12465/03_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_12465/03_2026/7nll_12465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nll_12465/03_2026/7nll_12465.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nll_12465/03_2026/7nll_12465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nll_12465/03_2026/7nll_12465.map" } 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-5986/lib/python3.9/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: 1.25, per 1000 atoms: 0.25 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: 0.42 Conformation dependent library (CDL) restraints added in 287.2 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: 0.17 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: 0.71 Time building geometry restraints manager: 0.55 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 - 22.37: 2892 22.37 - 44.73: 96 44.73 - 67.10: 14 67.10 - 89.47: 12 89.47 - 111.84: 14 Dihedral angle restraints: 3028 sinusoidal: 1140 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=" C2 RTV D1001 " pdb=" C3 RTV D1001 " pdb=" C4 RTV D1001 " pdb=" C5 RTV D1001 " ideal model delta sinusoidal sigma weight residual -57.83 54.01 -111.84 1 3.00e+01 1.11e-03 1.46e+01 ... (remaining 3025 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: 0.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.260 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 15.471 111.836 1814 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 covalent geometry : bond 0.00274 ( 5196) covalent geometry : angle 0.54912 ( 7082) SS BOND : bond 0.00204 ( 10) SS BOND : angle 0.71170 ( 20) hydrogen bonds : bond 0.23601 ( 171) hydrogen bonds : angle 9.26000 ( 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 : 0.194 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: 0.4870 time to fit residues: 82.8429 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 : 0.174 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN C 39 GLN C 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.103136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087963 restraints weight = 8625.235| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.73 r_work: 0.3163 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5206 Z= 0.126 Angle : 0.547 5.695 7102 Z= 0.292 Chirality : 0.046 0.246 747 Planarity : 0.004 0.040 927 Dihedral : 6.619 40.645 770 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.68 % Allowed : 14.37 % 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: 1.12 (0.31), residues: 648 helix: -0.72 (0.82), residues: 38 sheet: 2.58 (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 0.010 0.001 TRP C 116 HIS 0.000 0.000 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5196) covalent geometry : angle 0.54314 ( 7082) SS BOND : bond 0.00237 ( 10) SS BOND : angle 1.30284 ( 20) hydrogen bonds : bond 0.04073 ( 171) hydrogen bonds : angle 6.97859 ( 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 143 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: B 417 LYS cc_start: 0.8282 (ttmm) cc_final: 0.8070 (ttmt) REVERT: B 418 ILE cc_start: 0.8151 (mp) cc_final: 0.7909 (mm) REVERT: B 420 ASP cc_start: 0.8728 (m-30) cc_final: 0.8457 (m-30) REVERT: B 465 GLU cc_start: 0.8899 (tt0) cc_final: 0.8475 (tt0) REVERT: D 420 ASP cc_start: 0.8756 (m-30) cc_final: 0.8452 (m-30) REVERT: D 493 GLN cc_start: 0.8365 (tp40) cc_final: 0.8021 (tp40) REVERT: D 498 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: A 6 GLU cc_start: 0.7496 (mp0) cc_final: 0.7221 (mp0) REVERT: A 31 ASP cc_start: 0.8171 (t0) cc_final: 0.7910 (t0) REVERT: A 46 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7788 (pt0) REVERT: A 73 ASP cc_start: 0.8087 (t0) cc_final: 0.7807 (t0) REVERT: C 32 TYR cc_start: 0.9130 (m-80) cc_final: 0.8820 (m-80) REVERT: C 84 ASN cc_start: 0.8703 (m110) cc_final: 0.8485 (m-40) REVERT: C 90 ASP cc_start: 0.7917 (m-30) cc_final: 0.7681 (m-30) REVERT: C 95 TYR cc_start: 0.9327 (m-80) cc_final: 0.8951 (m-80) outliers start: 14 outliers final: 4 residues processed: 135 average time/residue: 0.3798 time to fit residues: 53.9862 Evaluate side-chains 125 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 3 optimal weight: 30.0000 chunk 9 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 501 ASN D 487 ASN A 74 ASN A 82 GLN C 3 GLN C 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.098070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.082578 restraints weight = 8770.927| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.81 r_work: 0.3012 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3435 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= 0.253 Angle : 0.617 5.542 7102 Z= 0.330 Chirality : 0.046 0.165 747 Planarity : 0.005 0.037 927 Dihedral : 5.789 41.035 770 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.36 % Allowed : 14.94 % 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: 0.45 (0.31), residues: 648 helix: -1.10 (0.76), residues: 37 sheet: 1.54 (0.36), residues: 187 loop : -0.13 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 19 TYR 0.020 0.002 TYR B 495 PHE 0.013 0.002 PHE A 68 TRP 0.010 0.002 TRP A 121 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00582 ( 5196) covalent geometry : angle 0.61310 ( 7082) SS BOND : bond 0.00539 ( 10) SS BOND : angle 1.40244 ( 20) hydrogen bonds : bond 0.04341 ( 171) hydrogen bonds : angle 6.90843 ( 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 155 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 418 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8179 (mm) REVERT: B 493 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: B 498 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8316 (mp10) REVERT: D 420 ASP cc_start: 0.8983 (m-30) cc_final: 0.8748 (m-30) REVERT: D 493 GLN cc_start: 0.8615 (tp40) cc_final: 0.8319 (tp40) REVERT: D 498 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8390 (mp10) REVERT: A 6 GLU cc_start: 0.8195 (mp0) cc_final: 0.7679 (mp0) REVERT: A 46 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8341 (pt0) REVERT: A 73 ASP cc_start: 0.8248 (t0) cc_final: 0.7949 (t0) REVERT: A 76 LYS cc_start: 0.8297 (mtpm) cc_final: 0.7966 (mtmm) REVERT: A 103 SER cc_start: 0.8721 (m) cc_final: 0.8461 (p) REVERT: A 108 THR cc_start: 0.9442 (m) cc_final: 0.9217 (p) REVERT: A 128 THR cc_start: 0.8810 (m) cc_final: 0.8560 (p) REVERT: C 31 ASP cc_start: 0.8626 (t0) cc_final: 0.8419 (t0) REVERT: C 32 TYR cc_start: 0.9235 (m-80) cc_final: 0.8881 (m-80) REVERT: C 46 GLU cc_start: 0.8586 (pt0) cc_final: 0.8382 (pt0) REVERT: C 84 ASN cc_start: 0.8722 (m110) cc_final: 0.8483 (m-40) REVERT: C 90 ASP cc_start: 0.8184 (m-30) cc_final: 0.7853 (m-30) REVERT: C 95 TYR cc_start: 0.9369 (m-80) cc_final: 0.8982 (m-80) outliers start: 28 outliers final: 11 residues processed: 141 average time/residue: 0.3741 time to fit residues: 55.6381 Evaluate side-chains 126 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 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 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 492 LEU 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: 7.9990 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 14 optimal weight: 0.2980 chunk 26 optimal weight: 9.9990 overall best weight: 6.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN C 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.082983 restraints weight = 8723.213| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.83 r_work: 0.3017 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3630 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= 0.181 Angle : 0.577 8.303 7102 Z= 0.303 Chirality : 0.044 0.159 747 Planarity : 0.004 0.034 927 Dihedral : 5.616 40.330 770 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.79 % Allowed : 19.35 % Favored : 75.86 % 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: 0.12 (0.31), residues: 648 helix: -1.45 (0.81), residues: 32 sheet: 1.23 (0.37), residues: 187 loop : -0.32 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 403 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 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 5196) covalent geometry : angle 0.57426 ( 7082) SS BOND : bond 0.00284 ( 10) SS BOND : angle 1.13042 ( 20) hydrogen bonds : bond 0.03736 ( 171) hydrogen bonds : angle 6.60068 ( 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 140 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: B 498 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8322 (mp10) REVERT: D 420 ASP cc_start: 0.8937 (m-30) cc_final: 0.8626 (m-30) REVERT: D 493 GLN cc_start: 0.8636 (tp40) cc_final: 0.8325 (tp40) REVERT: D 498 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8393 (mp10) REVERT: A 6 GLU cc_start: 0.8267 (mp0) cc_final: 0.7803 (mp0) REVERT: A 46 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8345 (pt0) REVERT: A 103 SER cc_start: 0.8877 (m) cc_final: 0.8597 (p) REVERT: C 31 ASP cc_start: 0.8655 (t0) cc_final: 0.8366 (t0) REVERT: C 32 TYR cc_start: 0.9210 (m-80) cc_final: 0.8900 (m-80) REVERT: C 84 ASN cc_start: 0.8711 (m110) cc_final: 0.8458 (m-40) REVERT: C 90 ASP cc_start: 0.8210 (m-30) cc_final: 0.7833 (m-30) REVERT: C 95 TYR cc_start: 0.9381 (m-80) cc_final: 0.8970 (m-80) outliers start: 25 outliers final: 16 residues processed: 127 average time/residue: 0.3505 time to fit residues: 47.1615 Evaluate side-chains 126 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain C residue 129 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: 0.0030 chunk 55 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN C 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.102010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.086516 restraints weight = 8710.642| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.82 r_work: 0.3080 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5206 Z= 0.109 Angle : 0.519 9.524 7102 Z= 0.270 Chirality : 0.042 0.140 747 Planarity : 0.004 0.032 927 Dihedral : 5.079 41.391 770 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.02 % Allowed : 20.88 % 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: 0.10 (0.31), residues: 648 helix: -1.12 (0.88), residues: 31 sheet: 1.19 (0.37), residues: 187 loop : -0.35 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 403 TYR 0.016 0.001 TYR B 369 PHE 0.021 0.001 PHE D 486 TRP 0.009 0.001 TRP D 436 HIS 0.000 0.000 HIS D 519 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5196) covalent geometry : angle 0.51803 ( 7082) SS BOND : bond 0.00245 ( 10) SS BOND : angle 0.76196 ( 20) hydrogen bonds : bond 0.03163 ( 171) hydrogen bonds : angle 6.22220 ( 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 137 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: B 498 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8088 (mp10) REVERT: D 420 ASP cc_start: 0.8904 (m-30) cc_final: 0.8587 (m-30) REVERT: D 493 GLN cc_start: 0.8635 (tp40) cc_final: 0.8326 (tp40) REVERT: D 498 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8265 (mp10) REVERT: A 6 GLU cc_start: 0.8227 (mp0) cc_final: 0.7673 (mp0) REVERT: A 46 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8333 (pt0) REVERT: A 80 TYR cc_start: 0.8615 (m-80) cc_final: 0.8410 (m-80) REVERT: A 103 SER cc_start: 0.8837 (m) cc_final: 0.8631 (p) REVERT: C 31 ASP cc_start: 0.8568 (t0) cc_final: 0.8321 (t0) REVERT: C 32 TYR cc_start: 0.9130 (m-80) cc_final: 0.8875 (m-80) REVERT: C 84 ASN cc_start: 0.8738 (m110) cc_final: 0.8497 (m-40) REVERT: C 90 ASP cc_start: 0.8250 (m-30) cc_final: 0.7884 (m-30) REVERT: C 95 TYR cc_start: 0.9360 (m-80) cc_final: 0.8965 (m-80) REVERT: C 123 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7870 (pp30) outliers start: 21 outliers final: 15 residues processed: 128 average time/residue: 0.3931 time to fit residues: 53.0953 Evaluate side-chains 127 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 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 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 498 GLN Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 43 LYS 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 C residue 11 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 123 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN C 3 GLN C 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.083351 restraints weight = 8806.843| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.82 r_work: 0.3021 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 : 0.004 0.021 5206 Z= 0.186 Angle : 0.563 10.375 7102 Z= 0.294 Chirality : 0.044 0.157 747 Planarity : 0.004 0.037 927 Dihedral : 5.393 39.734 770 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 5.36 % Allowed : 20.69 % Favored : 73.95 % 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: -0.07 (0.31), residues: 648 helix: -1.15 (0.87), residues: 31 sheet: 0.95 (0.36), residues: 187 loop : -0.41 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 457 TYR 0.015 0.001 TYR B 369 PHE 0.010 0.001 PHE A 68 TRP 0.007 0.001 TRP C 116 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 5196) covalent geometry : angle 0.56082 ( 7082) SS BOND : bond 0.00346 ( 10) SS BOND : angle 1.01091 ( 20) hydrogen bonds : bond 0.03507 ( 171) hydrogen bonds : angle 6.45765 ( 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 142 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8793 (m-30) cc_final: 0.8511 (m-30) REVERT: B 457 ARG cc_start: 0.9085 (ttt90) cc_final: 0.8833 (ttt90) REVERT: B 493 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: B 498 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8211 (mp10) REVERT: D 420 ASP cc_start: 0.8878 (m-30) cc_final: 0.8570 (m-30) REVERT: D 493 GLN cc_start: 0.8628 (tp40) cc_final: 0.8415 (tp40) REVERT: D 498 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8391 (mp10) REVERT: A 6 GLU cc_start: 0.8390 (mp0) cc_final: 0.7862 (mp0) REVERT: A 46 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8403 (pt0) REVERT: C 31 ASP cc_start: 0.8660 (t0) cc_final: 0.8415 (t0) REVERT: C 32 TYR cc_start: 0.9191 (m-80) cc_final: 0.8923 (m-80) REVERT: C 46 GLU cc_start: 0.8620 (pt0) cc_final: 0.8394 (pt0) REVERT: C 84 ASN cc_start: 0.8725 (m110) cc_final: 0.8503 (m-40) REVERT: C 90 ASP cc_start: 0.8272 (m-30) cc_final: 0.7882 (m-30) REVERT: C 95 TYR cc_start: 0.9364 (m-80) cc_final: 0.8978 (m-80) REVERT: C 123 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7788 (pp30) outliers start: 28 outliers final: 17 residues processed: 129 average time/residue: 0.3407 time to fit residues: 46.5740 Evaluate side-chains 130 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 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 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 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 123 GLN 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: 5.9990 chunk 26 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3423 r_free = 0.3423 target = 0.100018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.084493 restraints weight = 8648.709| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.80 r_work: 0.3039 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5206 Z= 0.144 Angle : 0.548 12.069 7102 Z= 0.284 Chirality : 0.043 0.147 747 Planarity : 0.004 0.037 927 Dihedral : 5.197 40.370 770 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 6.13 % Allowed : 21.84 % Favored : 72.03 % 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 (0.31), residues: 648 helix: -1.15 (0.88), residues: 31 sheet: 0.85 (0.36), residues: 187 loop : -0.39 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 403 TYR 0.016 0.001 TYR B 369 PHE 0.007 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 covalent geometry : bond 0.00332 ( 5196) covalent geometry : angle 0.54662 ( 7082) SS BOND : bond 0.00265 ( 10) SS BOND : angle 0.86742 ( 20) hydrogen bonds : bond 0.03245 ( 171) hydrogen bonds : angle 6.30946 ( 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 141 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8778 (m-30) cc_final: 0.8490 (m-30) REVERT: B 493 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7618 (tm-30) REVERT: B 498 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8184 (mp10) REVERT: D 420 ASP cc_start: 0.8889 (m-30) cc_final: 0.8548 (m-30) REVERT: D 493 GLN cc_start: 0.8647 (tp40) cc_final: 0.8384 (tp40) REVERT: D 498 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8333 (mp10) REVERT: A 6 GLU cc_start: 0.8343 (mp0) cc_final: 0.7806 (mp0) REVERT: A 31 ASP cc_start: 0.8363 (t0) cc_final: 0.8002 (t0) REVERT: A 45 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7734 (mtt180) REVERT: A 46 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8408 (pt0) REVERT: A 76 LYS cc_start: 0.8256 (mtmm) cc_final: 0.7985 (ptpp) REVERT: C 31 ASP cc_start: 0.8694 (t0) cc_final: 0.8340 (t0) REVERT: C 32 TYR cc_start: 0.9171 (m-80) cc_final: 0.8888 (m-80) REVERT: C 46 GLU cc_start: 0.8616 (pt0) cc_final: 0.8410 (pt0) REVERT: C 84 ASN cc_start: 0.8688 (m110) cc_final: 0.8477 (m-40) REVERT: C 90 ASP cc_start: 0.8271 (m-30) cc_final: 0.7902 (m-30) REVERT: C 95 TYR cc_start: 0.9377 (m-80) cc_final: 0.9069 (m-80) outliers start: 32 outliers final: 20 residues processed: 130 average time/residue: 0.3629 time to fit residues: 49.9594 Evaluate side-chains 129 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 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 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 30 ASP 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 69 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain C residue 11 LEU 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: 8.9990 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 14 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3440 r_free = 0.3440 target = 0.100998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.085408 restraints weight = 8644.299| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.81 r_work: 0.3059 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5206 Z= 0.116 Angle : 0.536 12.534 7102 Z= 0.275 Chirality : 0.042 0.139 747 Planarity : 0.004 0.035 927 Dihedral : 5.000 41.025 770 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.60 % Allowed : 22.99 % 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: -0.05 (0.31), residues: 648 helix: -1.02 (0.92), residues: 31 sheet: 1.03 (0.37), residues: 177 loop : -0.41 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.016 0.001 TYR B 369 PHE 0.005 0.001 PHE D 490 TRP 0.009 0.001 TRP D 436 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5196) covalent geometry : angle 0.53496 ( 7082) SS BOND : bond 0.00231 ( 10) SS BOND : angle 0.81930 ( 20) hydrogen bonds : bond 0.03067 ( 171) hydrogen bonds : angle 6.13084 ( 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 129 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: B 498 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8126 (mp10) REVERT: B 517 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8673 (tt) REVERT: D 420 ASP cc_start: 0.8881 (m-30) cc_final: 0.8555 (m-30) REVERT: D 493 GLN cc_start: 0.8655 (tp40) cc_final: 0.8320 (tp40) REVERT: D 498 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8282 (mp10) REVERT: D 517 LEU cc_start: 0.8086 (tp) cc_final: 0.7856 (tt) REVERT: A 6 GLU cc_start: 0.7739 (mp0) cc_final: 0.7410 (mp0) REVERT: A 31 ASP cc_start: 0.8372 (t0) cc_final: 0.7974 (t0) REVERT: A 45 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7731 (mtt180) REVERT: A 76 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7900 (ptpp) REVERT: C 31 ASP cc_start: 0.8679 (t0) cc_final: 0.8366 (t0) REVERT: C 32 TYR cc_start: 0.9171 (m-80) cc_final: 0.8925 (m-80) REVERT: C 46 GLU cc_start: 0.8630 (pt0) cc_final: 0.8408 (pt0) REVERT: C 84 ASN cc_start: 0.8655 (m110) cc_final: 0.8447 (m-40) REVERT: C 90 ASP cc_start: 0.8283 (m-30) cc_final: 0.7875 (m-30) outliers start: 24 outliers final: 19 residues processed: 119 average time/residue: 0.3832 time to fit residues: 48.2742 Evaluate side-chains 129 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 498 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU 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 418 ILE 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 65 LYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 79 VAL 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: 0.2980 chunk 62 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 14 optimal weight: 0.0970 chunk 19 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 overall best weight: 3.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.101006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.085565 restraints weight = 8592.696| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.76 r_work: 0.3097 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4131 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= 0.121 Angle : 0.538 11.891 7102 Z= 0.277 Chirality : 0.043 0.138 747 Planarity : 0.004 0.034 927 Dihedral : 4.916 40.834 770 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.41 % Allowed : 22.80 % 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: -0.06 (0.31), residues: 648 helix: -0.98 (0.92), residues: 31 sheet: 1.01 (0.36), residues: 177 loop : -0.41 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.016 0.001 TYR B 369 PHE 0.005 0.001 PHE B 490 TRP 0.008 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 5196) covalent geometry : angle 0.53723 ( 7082) SS BOND : bond 0.00235 ( 10) SS BOND : angle 0.81662 ( 20) hydrogen bonds : bond 0.03050 ( 171) hydrogen bonds : angle 6.05234 ( 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 132 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 408 ARG cc_start: 0.9138 (tmm160) cc_final: 0.8713 (ppt170) REVERT: B 493 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: D 420 ASP cc_start: 0.8865 (m-30) cc_final: 0.8541 (m-30) REVERT: D 493 GLN cc_start: 0.8617 (tp40) cc_final: 0.8356 (tp40) REVERT: D 498 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8263 (mp10) REVERT: D 517 LEU cc_start: 0.8147 (tp) cc_final: 0.7936 (tt) REVERT: A 6 GLU cc_start: 0.7785 (mp0) cc_final: 0.7357 (mp0) REVERT: A 31 ASP cc_start: 0.8354 (t0) cc_final: 0.7900 (t0) REVERT: A 45 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7682 (mtt180) REVERT: A 73 ASP cc_start: 0.7996 (t0) cc_final: 0.7611 (t0) REVERT: A 76 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7987 (ptpp) REVERT: C 31 ASP cc_start: 0.8705 (t0) cc_final: 0.8457 (t0) REVERT: C 32 TYR cc_start: 0.9174 (m-80) cc_final: 0.8952 (m-80) REVERT: C 46 GLU cc_start: 0.8636 (pt0) cc_final: 0.8414 (pt0) REVERT: C 90 ASP cc_start: 0.8294 (m-30) cc_final: 0.7880 (m-30) REVERT: C 95 TYR cc_start: 0.9335 (m-80) cc_final: 0.9122 (m-80) outliers start: 23 outliers final: 18 residues processed: 122 average time/residue: 0.3667 time to fit residues: 47.4556 Evaluate side-chains 127 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 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 418 ILE 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 45 ARG 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 C residue 11 LEU Chi-restraints excluded: chain C residue 79 VAL 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: 7.9990 chunk 50 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.098247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.082834 restraints weight = 8663.042| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.78 r_work: 0.3012 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5206 Z= 0.190 Angle : 0.620 16.972 7102 Z= 0.309 Chirality : 0.044 0.153 747 Planarity : 0.004 0.034 927 Dihedral : 5.322 39.129 770 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.02 % Allowed : 23.18 % 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: -0.26 (0.31), residues: 648 helix: -1.06 (1.04), residues: 25 sheet: 0.72 (0.36), residues: 187 loop : -0.52 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 457 TYR 0.015 0.001 TYR B 369 PHE 0.009 0.001 PHE A 68 TRP 0.006 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 5196) covalent geometry : angle 0.61844 ( 7082) SS BOND : bond 0.00316 ( 10) SS BOND : angle 1.03088 ( 20) hydrogen bonds : bond 0.03458 ( 171) hydrogen bonds : angle 6.32981 ( 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 129 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8815 (m-30) cc_final: 0.8511 (m-30) REVERT: B 493 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: D 403 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8437 (ttp-170) REVERT: D 420 ASP cc_start: 0.8866 (m-30) cc_final: 0.8611 (m-30) REVERT: D 493 GLN cc_start: 0.8634 (tp40) cc_final: 0.8358 (tp40) REVERT: D 498 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8355 (mp10) REVERT: D 517 LEU cc_start: 0.8203 (tp) cc_final: 0.7999 (tt) REVERT: A 6 GLU cc_start: 0.7884 (mp0) cc_final: 0.7495 (mp0) REVERT: A 31 ASP cc_start: 0.8313 (t0) cc_final: 0.7838 (t0) REVERT: A 45 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7730 (mtt180) REVERT: C 31 ASP cc_start: 0.8796 (t0) cc_final: 0.8457 (t0) REVERT: C 32 TYR cc_start: 0.9295 (m-80) cc_final: 0.9050 (m-80) REVERT: C 46 GLU cc_start: 0.8632 (pt0) cc_final: 0.8417 (pt0) REVERT: C 90 ASP cc_start: 0.8295 (m-30) cc_final: 0.7907 (m-30) outliers start: 21 outliers final: 17 residues processed: 121 average time/residue: 0.3264 time to fit residues: 42.0044 Evaluate side-chains 122 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 493 GLN Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 403 ARG 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 30 ASP Chi-restraints excluded: chain A residue 45 ARG 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 C residue 3 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 79 VAL 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: 3.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 0.0370 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 32 optimal weight: 20.0000 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.101661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.086120 restraints weight = 8651.607| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.81 r_work: 0.3107 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5206 Z= 0.098 Angle : 0.557 15.389 7102 Z= 0.279 Chirality : 0.042 0.132 747 Planarity : 0.003 0.032 927 Dihedral : 4.896 42.365 770 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.64 % Allowed : 24.33 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.31), residues: 648 helix: -0.93 (1.10), residues: 25 sheet: 0.92 (0.37), residues: 177 loop : -0.52 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 403 TYR 0.019 0.001 TYR C 95 PHE 0.005 0.001 PHE D 374 TRP 0.009 0.001 TRP D 436 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 5196) covalent geometry : angle 0.55620 ( 7082) SS BOND : bond 0.00179 ( 10) SS BOND : angle 0.70776 ( 20) hydrogen bonds : bond 0.02922 ( 171) hydrogen bonds : angle 6.06873 ( 417) =============================================================================== Job complete usr+sys time: 1819.08 seconds wall clock time: 31 minutes 33.57 seconds (1893.57 seconds total)