Starting phenix.real_space_refine on Wed Feb 12 07:29:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nll_12465/02_2025/7nll_12465.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nll_12465/02_2025/7nll_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7nll_12465/02_2025/7nll_12465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nll_12465/02_2025/7nll_12465.map" model { file = "/net/cci-nas-00/data/ceres_data/7nll_12465/02_2025/7nll_12465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nll_12465/02_2025/7nll_12465.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG: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: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG: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: 3.39, per 1000 atoms: 0.67 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: 1.03 Conformation dependent library (CDL) restraints added in 689.9 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: 0.62 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: 1.51 Time building geometry restraints manager: 1.16 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: 0.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.430 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:16.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.190 ------------------------------------------------------------------------------- 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 5196 Z= 0.176 Angle : 0.549 4.419 7082 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.002 TRP C 116 HIS 0.000 0.000 HIS B 519 PHE 0.012 0.001 PHE B 347 TYR 0.016 0.001 TYR C 109 ARG 0.002 0.000 ARG A 19 *********************** 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 : 0.588 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: 0.7738 (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: 0.8781 (m-80) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 1.0560 time to fit residues: 180.3980 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 : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 58 optimal weight: 20.0000 overall best weight: 10.1992 ------------------------------------------------------------------------------- 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** 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 = 0.3406 r_free = 0.3406 target = 0.095596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.080450 restraints weight = 8738.162| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.74 r_work: 0.3022 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5196 Z= 0.424 Angle : 0.652 7.606 7082 Z= 0.348 Chirality : 0.050 0.302 747 Planarity : 0.005 0.035 927 Dihedral : 6.811 43.896 770 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 4.21 % Allowed : 12.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.31), residues: 648 helix: -0.94 (0.79), residues: 37 sheet: 1.30 (0.37), residues: 201 loop : 0.07 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 116 HIS 0.001 0.001 HIS B 519 PHE 0.017 0.002 PHE D 347 TYR 0.022 0.002 TYR B 495 ARG 0.004 0.001 ARG C 19 *********************** 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 151 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8769 (m-30) cc_final: 0.8467 (m-30) REVERT: D 340 GLU cc_start: 0.8416 (tt0) cc_final: 0.8134 (tm-30) REVERT: D 420 ASP cc_start: 0.8918 (m-30) cc_final: 0.8580 (m-30) REVERT: D 493 GLN cc_start: 0.8538 (tp40) cc_final: 0.8220 (tp40) REVERT: D 498 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8402 (mp10) REVERT: A 6 GLU cc_start: 0.8071 (mp0) cc_final: 0.7678 (mp0) REVERT: A 31 ASP cc_start: 0.8307 (t0) cc_final: 0.8067 (t0) REVERT: A 46 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8194 (pt0) REVERT: A 73 ASP cc_start: 0.8223 (t0) cc_final: 0.8001 (t0) REVERT: A 108 THR cc_start: 0.9431 (m) cc_final: 0.9121 (p) REVERT: A 128 THR cc_start: 0.8805 (m) cc_final: 0.8561 (p) REVERT: C 32 TYR cc_start: 0.9219 (m-80) cc_final: 0.8890 (m-80) REVERT: C 84 ASN cc_start: 0.8744 (m110) cc_final: 0.8538 (m-40) REVERT: C 90 ASP cc_start: 0.8133 (m-30) cc_final: 0.7830 (m-30) REVERT: C 95 TYR cc_start: 0.9363 (m-80) cc_final: 0.8913 (m-80) outliers start: 22 outliers final: 5 residues processed: 136 average time/residue: 0.8468 time to fit residues: 121.7742 Evaluate side-chains 118 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain D residue 345 THR 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 57 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 34 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN B 501 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN A 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.080936 restraints weight = 8663.957| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.74 r_work: 0.3028 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5196 Z= 0.273 Angle : 0.568 8.275 7082 Z= 0.301 Chirality : 0.044 0.159 747 Planarity : 0.004 0.035 927 Dihedral : 5.840 40.965 770 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.83 % Allowed : 18.01 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.31), residues: 648 helix: -1.26 (0.77), residues: 37 sheet: 1.31 (0.36), residues: 187 loop : -0.22 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 116 HIS 0.001 0.001 HIS B 519 PHE 0.009 0.001 PHE A 68 TYR 0.017 0.001 TYR B 369 ARG 0.008 0.001 ARG B 403 *********************** 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 140 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 418 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8116 (mm) REVERT: B 420 ASP cc_start: 0.8833 (m-30) cc_final: 0.8540 (m-30) REVERT: B 493 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: D 340 GLU cc_start: 0.8499 (tt0) cc_final: 0.8192 (tm-30) REVERT: D 420 ASP cc_start: 0.8942 (m-30) cc_final: 0.8639 (m-30) REVERT: D 493 GLN cc_start: 0.8612 (tp40) cc_final: 0.8295 (tp40) REVERT: D 498 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8375 (mp10) REVERT: A 6 GLU cc_start: 0.8171 (mp0) cc_final: 0.7643 (mp0) REVERT: A 46 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8271 (pt0) REVERT: A 73 ASP cc_start: 0.8194 (t0) cc_final: 0.7933 (t0) REVERT: A 103 SER cc_start: 0.8702 (m) cc_final: 0.8448 (p) REVERT: C 32 TYR cc_start: 0.9213 (m-80) cc_final: 0.8935 (m-80) REVERT: C 84 ASN cc_start: 0.8730 (m110) cc_final: 0.8486 (m-40) REVERT: C 90 ASP cc_start: 0.8182 (m-30) cc_final: 0.7863 (m-30) REVERT: C 95 TYR cc_start: 0.9360 (m-80) cc_final: 0.8992 (m-80) outliers start: 20 outliers final: 11 residues processed: 129 average time/residue: 0.8340 time to fit residues: 113.8637 Evaluate side-chains 127 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 418 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 D residue 333 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 112 SER Chi-restraints excluded: chain C residue 57 SER 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 18 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 2 optimal weight: 30.0000 chunk 35 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.097857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.082454 restraints weight = 8818.278| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.82 r_work: 0.3008 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5196 Z= 0.277 Angle : 0.563 9.389 7082 Z= 0.296 Chirality : 0.044 0.163 747 Planarity : 0.004 0.033 927 Dihedral : 5.677 40.295 770 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.75 % Allowed : 17.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.31), residues: 648 helix: -1.41 (0.84), residues: 31 sheet: 1.05 (0.36), residues: 187 loop : -0.32 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 116 HIS 0.001 0.000 HIS B 519 PHE 0.010 0.001 PHE A 68 TYR 0.016 0.001 TYR B 369 ARG 0.004 0.000 ARG B 403 *********************** 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 149 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 457 ARG cc_start: 0.9132 (ttt90) cc_final: 0.8904 (ttt90) REVERT: B 493 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: D 340 GLU cc_start: 0.8586 (tt0) cc_final: 0.8160 (tm-30) REVERT: D 420 ASP cc_start: 0.8946 (m-30) cc_final: 0.8655 (m-30) REVERT: D 493 GLN cc_start: 0.8625 (tp40) cc_final: 0.8346 (tp40) REVERT: D 498 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8412 (mp10) REVERT: A 6 GLU cc_start: 0.8307 (mp0) cc_final: 0.7856 (mp0) REVERT: A 46 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8381 (pt0) REVERT: A 73 ASP cc_start: 0.8210 (t0) cc_final: 0.7928 (t0) REVERT: A 76 LYS cc_start: 0.8200 (mtpm) cc_final: 0.7919 (mtmm) REVERT: A 103 SER cc_start: 0.8895 (m) cc_final: 0.8684 (p) REVERT: C 32 TYR cc_start: 0.9238 (m-80) cc_final: 0.8927 (m-80) REVERT: C 84 ASN cc_start: 0.8702 (m110) cc_final: 0.8472 (m-40) REVERT: C 90 ASP cc_start: 0.8229 (m-30) cc_final: 0.7889 (m-30) REVERT: C 95 TYR cc_start: 0.9378 (m-80) cc_final: 0.8966 (m-80) outliers start: 30 outliers final: 21 residues processed: 135 average time/residue: 0.8234 time to fit residues: 117.6478 Evaluate side-chains 137 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 28 THR 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 57 SER 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 35 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 14 optimal weight: 0.0570 overall best weight: 6.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN A 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.097129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.081811 restraints weight = 8732.452| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.81 r_work: 0.2999 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5196 Z= 0.277 Angle : 0.565 10.584 7082 Z= 0.296 Chirality : 0.044 0.159 747 Planarity : 0.004 0.035 927 Dihedral : 5.534 39.932 770 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 6.51 % Allowed : 19.16 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.31), residues: 648 helix: -1.53 (0.82), residues: 31 sheet: 0.88 (0.36), residues: 187 loop : -0.40 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 PHE 0.009 0.001 PHE A 68 TYR 0.016 0.001 TYR B 369 ARG 0.003 0.000 ARG D 457 *********************** 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 150 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7642 (tm-30) REVERT: D 340 GLU cc_start: 0.8644 (tt0) cc_final: 0.8180 (tm-30) REVERT: D 420 ASP cc_start: 0.8929 (m-30) cc_final: 0.8621 (m-30) REVERT: D 493 GLN cc_start: 0.8624 (tp40) cc_final: 0.8290 (tp40) REVERT: D 498 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8388 (mp10) REVERT: A 6 GLU cc_start: 0.8369 (mp0) cc_final: 0.7850 (mp0) REVERT: A 46 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8380 (pt0) REVERT: A 76 LYS cc_start: 0.8336 (mtpm) cc_final: 0.8114 (mtmm) REVERT: C 32 TYR cc_start: 0.9228 (m-80) cc_final: 0.8914 (m-80) REVERT: C 84 ASN cc_start: 0.8725 (m110) cc_final: 0.8502 (m-40) REVERT: C 90 ASP cc_start: 0.8299 (m-30) cc_final: 0.7971 (m-30) REVERT: C 95 TYR cc_start: 0.9377 (m-80) cc_final: 0.9013 (m-80) outliers start: 34 outliers final: 23 residues processed: 132 average time/residue: 0.8098 time to fit residues: 113.3303 Evaluate side-chains 137 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 28 THR 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 65 LYS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.097314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.081894 restraints weight = 8686.548| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.79 r_work: 0.2995 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 5196 Z= 0.298 Angle : 0.575 11.493 7082 Z= 0.299 Chirality : 0.044 0.162 747 Planarity : 0.004 0.036 927 Dihedral : 5.576 39.351 770 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 6.51 % Allowed : 19.73 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.31), residues: 648 helix: -1.61 (0.84), residues: 30 sheet: 0.73 (0.36), residues: 187 loop : -0.43 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 PHE 0.010 0.001 PHE A 68 TYR 0.015 0.001 TYR B 369 ARG 0.003 0.000 ARG D 457 *********************** 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 150 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: B 498 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8398 (mp10) REVERT: D 340 GLU cc_start: 0.8710 (tt0) cc_final: 0.8173 (tm-30) REVERT: D 420 ASP cc_start: 0.8909 (m-30) cc_final: 0.8588 (m-30) REVERT: D 493 GLN cc_start: 0.8620 (tp40) cc_final: 0.8311 (tp40) REVERT: D 498 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8396 (mp10) REVERT: D 517 LEU cc_start: 0.8178 (tp) cc_final: 0.7961 (tt) REVERT: A 6 GLU cc_start: 0.8414 (mp0) cc_final: 0.7883 (mp0) REVERT: A 31 ASP cc_start: 0.8401 (t0) cc_final: 0.8008 (t0) REVERT: A 45 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7797 (mtt180) REVERT: A 46 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8407 (pt0) REVERT: C 32 TYR cc_start: 0.9248 (m-80) cc_final: 0.9013 (m-80) REVERT: C 46 GLU cc_start: 0.8630 (pt0) cc_final: 0.8415 (pt0) REVERT: C 82 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: C 84 ASN cc_start: 0.8693 (m110) cc_final: 0.8210 (m-40) REVERT: C 90 ASP cc_start: 0.8307 (m-30) cc_final: 0.7972 (m-30) REVERT: C 95 TYR cc_start: 0.9353 (m-80) cc_final: 0.9022 (m-80) outliers start: 34 outliers final: 21 residues processed: 130 average time/residue: 0.8190 time to fit residues: 112.7558 Evaluate side-chains 140 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 417 LYS 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 79 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 82 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 59 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 42 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 30.0000 chunk 55 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.100776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.085325 restraints weight = 8506.978| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.80 r_work: 0.3061 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5196 Z= 0.156 Angle : 0.528 10.499 7082 Z= 0.271 Chirality : 0.042 0.136 747 Planarity : 0.004 0.034 927 Dihedral : 4.976 41.172 770 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.98 % Allowed : 21.84 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.31), residues: 648 helix: -1.44 (0.87), residues: 31 sheet: 1.23 (0.37), residues: 167 loop : -0.42 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 HIS 0.000 0.000 HIS D 519 PHE 0.005 0.001 PHE B 490 TYR 0.016 0.001 TYR B 369 ARG 0.003 0.000 ARG B 403 *********************** 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 140 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: B 408 ARG cc_start: 0.9088 (tmm160) cc_final: 0.8787 (ptm-80) REVERT: B 420 ASP cc_start: 0.8803 (m-30) cc_final: 0.8576 (m-30) REVERT: B 468 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8366 (pp) REVERT: B 493 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: B 498 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8303 (mp10) REVERT: D 340 GLU cc_start: 0.8731 (tt0) cc_final: 0.8218 (tm-30) REVERT: D 420 ASP cc_start: 0.8864 (m-30) cc_final: 0.8562 (m-30) REVERT: D 493 GLN cc_start: 0.8624 (tp40) cc_final: 0.8311 (tp40) REVERT: D 498 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8251 (mp10) REVERT: D 517 LEU cc_start: 0.8119 (tp) cc_final: 0.7906 (tt) REVERT: A 6 GLU cc_start: 0.8349 (mp0) cc_final: 0.7771 (mp0) REVERT: A 31 ASP cc_start: 0.8287 (t0) cc_final: 0.7852 (t0) REVERT: A 45 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7736 (mtt180) REVERT: A 46 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8360 (pt0) REVERT: C 32 TYR cc_start: 0.9176 (m-80) cc_final: 0.8973 (m-80) REVERT: C 90 ASP cc_start: 0.8270 (m-30) cc_final: 0.7917 (m-30) REVERT: C 95 TYR cc_start: 0.9362 (m-80) cc_final: 0.9019 (m-80) outliers start: 26 outliers final: 17 residues processed: 131 average time/residue: 0.8404 time to fit residues: 116.2831 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 : 0.605 ------------------------------------------------------------------------------- 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 468 ILE 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 433 VAL 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 79 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 57 SER 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 43 optimal weight: 0.0870 chunk 35 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 57 optimal weight: 0.0670 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 overall best weight: 3.8302 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.099797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.084446 restraints weight = 8695.356| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.76 r_work: 0.3041 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5196 Z= 0.199 Angle : 0.580 16.060 7082 Z= 0.290 Chirality : 0.043 0.142 747 Planarity : 0.004 0.032 927 Dihedral : 4.999 40.608 770 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 5.17 % Allowed : 22.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.31), residues: 648 helix: -1.44 (0.88), residues: 31 sheet: 1.18 (0.37), residues: 167 loop : -0.42 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 PHE 0.006 0.001 PHE A 68 TYR 0.016 0.001 TYR B 369 ARG 0.002 0.000 ARG B 403 *********************** 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 137 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 408 ARG cc_start: 0.9054 (tmm160) cc_final: 0.8814 (ptm-80) REVERT: B 493 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: B 498 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8424 (mp10) REVERT: D 340 GLU cc_start: 0.8739 (tt0) cc_final: 0.8234 (tm-30) REVERT: D 420 ASP cc_start: 0.8891 (m-30) cc_final: 0.8571 (m-30) REVERT: D 493 GLN cc_start: 0.8649 (tp40) cc_final: 0.8355 (tp40) REVERT: D 498 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8263 (mp10) REVERT: D 517 LEU cc_start: 0.8131 (tp) cc_final: 0.7928 (tt) REVERT: A 6 GLU cc_start: 0.7825 (mp0) cc_final: 0.7472 (mp0) REVERT: A 31 ASP cc_start: 0.8313 (t0) cc_final: 0.7831 (t0) REVERT: A 45 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7744 (mtt180) REVERT: A 76 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7964 (ptpp) REVERT: C 32 TYR cc_start: 0.9201 (m-80) cc_final: 0.8978 (m-80) REVERT: C 46 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8275 (pt0) REVERT: C 90 ASP cc_start: 0.8326 (m-30) cc_final: 0.7949 (m-30) REVERT: C 95 TYR cc_start: 0.9368 (m-80) cc_final: 0.9058 (m-80) outliers start: 27 outliers final: 20 residues processed: 128 average time/residue: 0.8037 time to fit residues: 109.1626 Evaluate side-chains 135 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 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 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 79 VAL 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 57 SER 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 58 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 12 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 overall best weight: 6.2988 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.097746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.082419 restraints weight = 8584.109| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.75 r_work: 0.3005 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5196 Z= 0.277 Angle : 0.576 11.586 7082 Z= 0.298 Chirality : 0.043 0.153 747 Planarity : 0.004 0.032 927 Dihedral : 5.307 39.406 770 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.79 % Allowed : 22.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.31), residues: 648 helix: -1.43 (1.03), residues: 24 sheet: 0.63 (0.36), residues: 187 loop : -0.49 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 436 HIS 0.002 0.001 HIS B 519 PHE 0.008 0.001 PHE A 68 TYR 0.015 0.001 TYR B 369 ARG 0.002 0.000 ARG B 457 *********************** 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 136 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 408 ARG cc_start: 0.9041 (tmm160) cc_final: 0.8741 (ptm-80) REVERT: B 493 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: B 498 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8406 (mp10) REVERT: D 340 GLU cc_start: 0.8770 (tt0) cc_final: 0.8188 (tm-30) REVERT: D 405 ASP cc_start: 0.8794 (m-30) cc_final: 0.8371 (m-30) REVERT: D 420 ASP cc_start: 0.8855 (m-30) cc_final: 0.8518 (m-30) REVERT: D 493 GLN cc_start: 0.8633 (tp40) cc_final: 0.8344 (tp40) REVERT: D 498 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8342 (mp10) REVERT: A 6 GLU cc_start: 0.7903 (mp0) cc_final: 0.7520 (mp0) REVERT: A 31 ASP cc_start: 0.8337 (t0) cc_final: 0.7843 (t0) REVERT: A 45 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7763 (mtt180) REVERT: A 89 GLU cc_start: 0.8462 (mp0) cc_final: 0.8076 (mp0) REVERT: C 32 TYR cc_start: 0.9237 (m-80) cc_final: 0.8997 (m-80) REVERT: C 46 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8281 (pt0) REVERT: C 90 ASP cc_start: 0.8340 (m-30) cc_final: 0.7953 (m-30) REVERT: C 95 TYR cc_start: 0.9355 (m-80) cc_final: 0.8982 (m-80) outliers start: 25 outliers final: 20 residues processed: 126 average time/residue: 0.7839 time to fit residues: 105.0465 Evaluate side-chains 132 residues out of total 554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 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 433 VAL Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain A residue 11 LEU 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 69 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 57 SER 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 21 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 43 optimal weight: 0.4980 overall best weight: 3.4586 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.099550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.084277 restraints weight = 8580.542| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.75 r_work: 0.3041 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5196 Z= 0.186 Angle : 0.554 11.690 7082 Z= 0.284 Chirality : 0.043 0.137 747 Planarity : 0.004 0.031 927 Dihedral : 5.025 40.830 770 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.79 % Allowed : 22.61 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.31), residues: 648 helix: -1.64 (1.01), residues: 25 sheet: 1.05 (0.37), residues: 167 loop : -0.52 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 436 HIS 0.000 0.000 HIS B 519 PHE 0.005 0.001 PHE B 490 TYR 0.016 0.001 TYR B 369 ARG 0.002 0.000 ARG B 403 ********************** 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: 25 poor density : 107 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 493 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: B 498 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8344 (mp10) REVERT: D 340 GLU cc_start: 0.8774 (tt0) cc_final: 0.8550 (tt0) REVERT: D 420 ASP cc_start: 0.8841 (m-30) cc_final: 0.8508 (m-30) REVERT: D 493 GLN cc_start: 0.8633 (tp40) cc_final: 0.8343 (tp40) REVERT: D 498 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8285 (mp10) REVERT: A 6 GLU cc_start: 0.7768 (mp0) cc_final: 0.7324 (mp0) REVERT: A 31 ASP cc_start: 0.8264 (t0) cc_final: 0.7734 (t0) REVERT: A 45 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7732 (mtt180) REVERT: A 89 GLU cc_start: 0.8499 (mp0) cc_final: 0.8204 (mp0) REVERT: C 32 TYR cc_start: 0.9212 (m-80) cc_final: 0.8935 (m-80) REVERT: C 46 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8276 (pt0) REVERT: C 90 ASP cc_start: 0.8326 (m-30) cc_final: 0.7939 (m-30) REVERT: C 95 TYR cc_start: 0.9376 (m-80) cc_final: 0.9064 (m-80) outliers start: 25 outliers final: 19 residues processed: 121 average time/residue: 0.7838 time to fit residues: 100.5635 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 : 0.592 ------------------------------------------------------------------------------- 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 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 30 ASP Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 57 SER 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 35 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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** B 414 GLN 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 = 0.097913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.082706 restraints weight = 8733.311| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.76 r_work: 0.3012 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5196 Z= 0.254 Angle : 0.571 11.149 7082 Z= 0.295 Chirality : 0.044 0.147 747 Planarity : 0.004 0.032 927 Dihedral : 5.131 39.494 770 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.21 % Allowed : 23.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.31), residues: 648 helix: -1.57 (1.02), residues: 24 sheet: 0.94 (0.38), residues: 167 loop : -0.56 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 436 HIS 0.001 0.000 HIS B 519 PHE 0.008 0.001 PHE B 490 TYR 0.016 0.001 TYR B 369 ARG 0.001 0.000 ARG B 403 =============================================================================== Job complete usr+sys time: 3723.33 seconds wall clock time: 66 minutes 37.97 seconds (3997.97 seconds total)