Starting phenix.real_space_refine on Sat Oct 24 10:15:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y5i_72509/10_2026/9y5i_72509.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y5i_72509/10_2026/9y5i_72509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y5i_72509/10_2026/9y5i_72509.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y5i_72509/10_2026/9y5i_72509.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y5i_72509/10_2026/9y5i_72509.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y5i_72509/10_2026/9y5i_72509.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 8504 2.51 5 N 2052 2.21 5 O 2328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12964 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3241 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 4, 'TRANS': 395} Chain breaks: 3 Chain: "B" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3241 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 4, 'TRANS': 395} Chain breaks: 3 Chain: "C" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3241 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 4, 'TRANS': 395} Chain breaks: 3 Chain: "D" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3241 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 4, 'TRANS': 395} Chain breaks: 3 Time building chain proxies: 2.43, per 1000 atoms: 0.19 Number of scatterers: 12964 At special positions: 0 Unit cell: (110.39, 110.39, 106.24, 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 80 16.00 O 2328 8.00 N 2052 7.00 C 8504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.81 Conformation dependent library (CDL) restraints added in 519.3 milliseconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3056 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 67.6% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 65 through 106 Processing helix chain 'A' and resid 123 through 139 Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 194 through 201 removed outlier: 3.896A pdb=" N GLU A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 207 removed outlier: 4.272A pdb=" N TRP A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 212 Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.758A pdb=" N HIS A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 322 Processing helix chain 'A' and resid 347 through 370 Processing helix chain 'A' and resid 374 through 398 removed outlier: 4.717A pdb=" N CYS A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 440 Proline residue: A 415 - end of helix removed outlier: 4.058A pdb=" N MET A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE A 427 " --> pdb=" O CYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 462 Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 476 through 513 removed outlier: 3.696A pdb=" N TYR A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 106 Processing helix chain 'B' and resid 123 through 139 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 194 through 201 removed outlier: 3.896A pdb=" N GLU B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 207 removed outlier: 4.272A pdb=" N TRP B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.758A pdb=" N HIS B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 322 Processing helix chain 'B' and resid 347 through 370 Processing helix chain 'B' and resid 374 through 398 removed outlier: 4.716A pdb=" N CYS B 378 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 440 Proline residue: B 415 - end of helix removed outlier: 4.058A pdb=" N MET B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE B 427 " --> pdb=" O CYS B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 462 Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 476 through 513 removed outlier: 3.700A pdb=" N TYR B 496 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU B 499 " --> pdb=" O ILE B 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 106 Processing helix chain 'C' and resid 123 through 139 Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 194 through 201 removed outlier: 3.895A pdb=" N GLU C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 removed outlier: 4.271A pdb=" N TRP C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 212 Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.759A pdb=" N HIS C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 322 Processing helix chain 'C' and resid 347 through 370 Processing helix chain 'C' and resid 374 through 398 removed outlier: 4.716A pdb=" N CYS C 378 " --> pdb=" O ASN C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 440 Proline residue: C 415 - end of helix removed outlier: 4.060A pdb=" N MET C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE C 427 " --> pdb=" O CYS C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 462 Processing helix chain 'C' and resid 465 through 470 Processing helix chain 'C' and resid 476 through 513 removed outlier: 3.701A pdb=" N TYR C 496 " --> pdb=" O SER C 492 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU C 499 " --> pdb=" O ILE C 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 106 Processing helix chain 'D' and resid 123 through 139 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 194 through 201 removed outlier: 3.896A pdb=" N GLU D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 207 removed outlier: 4.272A pdb=" N TRP D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 212 Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.758A pdb=" N HIS D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 322 Processing helix chain 'D' and resid 347 through 370 Processing helix chain 'D' and resid 374 through 398 removed outlier: 4.716A pdb=" N CYS D 378 " --> pdb=" O ASN D 374 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY D 398 " --> pdb=" O ILE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 440 Proline residue: D 415 - end of helix removed outlier: 4.058A pdb=" N MET D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE D 427 " --> pdb=" O CYS D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 462 Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 476 through 513 removed outlier: 3.703A pdb=" N TYR D 496 " --> pdb=" O SER D 492 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU D 499 " --> pdb=" O ILE D 495 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AA5, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 121 Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 121 1063 hydrogen bonds defined for protein. 3093 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: 2.10 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3911 1.34 - 1.45: 2036 1.45 - 1.57: 7173 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 13232 Sorted by residual: bond pdb=" CG1 ILE D 495 " pdb=" CD1 ILE D 495 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.75e+00 bond pdb=" CG1 ILE C 495 " pdb=" CD1 ILE C 495 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.73e+00 bond pdb=" CG1 ILE B 495 " pdb=" CD1 ILE B 495 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.72e+00 bond pdb=" CG1 ILE A 495 " pdb=" CD1 ILE A 495 " ideal model delta sigma weight residual 1.513 1.462 0.051 3.90e-02 6.57e+02 1.69e+00 bond pdb=" CB MET D 465 " pdb=" CG MET D 465 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.22e+00 ... (remaining 13227 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 17452 1.44 - 2.88: 405 2.88 - 4.32: 35 4.32 - 5.76: 16 5.76 - 7.20: 4 Bond angle restraints: 17912 Sorted by residual: angle pdb=" C ASN B 143 " pdb=" N ILE B 144 " pdb=" CA ILE B 144 " ideal model delta sigma weight residual 122.66 120.25 2.41 9.70e-01 1.06e+00 6.20e+00 angle pdb=" C ASN C 143 " pdb=" N ILE C 144 " pdb=" CA ILE C 144 " ideal model delta sigma weight residual 122.66 120.25 2.41 9.70e-01 1.06e+00 6.16e+00 angle pdb=" C ASN D 143 " pdb=" N ILE D 144 " pdb=" CA ILE D 144 " ideal model delta sigma weight residual 122.66 120.25 2.41 9.70e-01 1.06e+00 6.16e+00 angle pdb=" C LYS A 275 " pdb=" N ASN A 276 " pdb=" CA ASN A 276 " ideal model delta sigma weight residual 121.70 126.14 -4.44 1.80e+00 3.09e-01 6.10e+00 angle pdb=" C ASN A 143 " pdb=" N ILE A 144 " pdb=" CA ILE A 144 " ideal model delta sigma weight residual 122.66 120.28 2.38 9.70e-01 1.06e+00 6.04e+00 ... (remaining 17907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 6917 16.88 - 33.75: 700 33.75 - 50.63: 119 50.63 - 67.51: 12 67.51 - 84.38: 12 Dihedral angle restraints: 7760 sinusoidal: 3036 harmonic: 4724 Sorted by residual: dihedral pdb=" CA LYS C 260 " pdb=" C LYS C 260 " pdb=" N ILE C 261 " pdb=" CA ILE C 261 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LYS A 260 " pdb=" C LYS A 260 " pdb=" N ILE A 261 " pdb=" CA ILE A 261 " ideal model delta harmonic sigma weight residual 180.00 159.32 20.68 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA LYS D 260 " pdb=" C LYS D 260 " pdb=" N ILE D 261 " pdb=" CA ILE D 261 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 7757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1447 0.036 - 0.072: 492 0.072 - 0.109: 140 0.109 - 0.145: 29 0.145 - 0.181: 4 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CB THR B 148 " pdb=" CA THR B 148 " pdb=" OG1 THR B 148 " pdb=" CG2 THR B 148 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CB THR A 148 " pdb=" CA THR A 148 " pdb=" OG1 THR A 148 " pdb=" CG2 THR A 148 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CB THR C 148 " pdb=" CA THR C 148 " pdb=" OG1 THR C 148 " pdb=" CG2 THR C 148 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 2109 not shown) Planarity restraints: 2176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 440 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO C 441 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 441 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 441 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 440 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A 441 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 440 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO D 441 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 441 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 441 " -0.020 5.00e-02 4.00e+02 ... (remaining 2173 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 255 2.70 - 3.25: 13029 3.25 - 3.80: 20911 3.80 - 4.35: 26308 4.35 - 4.90: 45696 Nonbonded interactions: 106199 Sorted by model distance: nonbonded pdb=" OH TYR C 428 " pdb=" O ALA C 453 " model vdw 2.145 3.040 nonbonded pdb=" OH TYR A 428 " pdb=" O ALA A 453 " model vdw 2.145 3.040 nonbonded pdb=" OH TYR D 428 " pdb=" O ALA D 453 " model vdw 2.145 3.040 nonbonded pdb=" OH TYR B 428 " pdb=" O ALA B 453 " model vdw 2.146 3.040 nonbonded pdb=" O TYR A 375 " pdb=" OG SER A 379 " model vdw 2.262 3.040 ... (remaining 106194 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.170 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13232 Z= 0.169 Angle : 0.536 7.204 17912 Z= 0.300 Chirality : 0.040 0.181 2112 Planarity : 0.003 0.035 2176 Dihedral : 13.776 84.383 4704 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: 1.76 (0.21), residues: 1568 helix: 2.30 (0.16), residues: 984 sheet: 0.14 (0.36), residues: 208 loop : -1.34 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 212 TYR 0.008 0.001 TYR C 122 PHE 0.014 0.002 PHE A 482 TRP 0.004 0.001 TRP A 480 HIS 0.005 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (13232) covalent geometry : angle 0.53627 / 0.30 (17912) hydrogen bonds : bond 0.13595 / 9.22 ( 967) hydrogen bonds : angle 6.87824 / 5.00 ( 3093) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.402 Fit side-chains REVERT: A 183 ASP cc_start: 0.6944 (t0) cc_final: 0.6711 (t0) REVERT: A 185 ASP cc_start: 0.7956 (m-30) cc_final: 0.7747 (m-30) REVERT: B 183 ASP cc_start: 0.6941 (t0) cc_final: 0.6733 (t0) REVERT: C 183 ASP cc_start: 0.6945 (t0) cc_final: 0.6736 (t0) REVERT: D 183 ASP cc_start: 0.6952 (t0) cc_final: 0.6709 (t0) REVERT: D 185 ASP cc_start: 0.7922 (m-30) cc_final: 0.7722 (m-30) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.0767 time to fit residues: 23.1870 Evaluate side-chains 151 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS ** A 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS ** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** C 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS ** D 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.203126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.158313 restraints weight = 14233.309| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.23 r_work: 0.3629 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 13232 Z= 0.197 Angle : 0.575 7.502 17912 Z= 0.314 Chirality : 0.041 0.146 2112 Planarity : 0.003 0.033 2176 Dihedral : 4.502 18.923 1720 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.65 % Allowed : 9.02 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.36 (0.21), residues: 1568 helix: 1.95 (0.16), residues: 1032 sheet: 0.16 (0.36), residues: 216 loop : -2.09 (0.27), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 484 TYR 0.013 0.001 TYR C 264 PHE 0.013 0.002 PHE D 494 TRP 0.003 0.001 TRP A 480 HIS 0.006 0.002 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (13232) covalent geometry : angle 0.57464 / 0.31 (17912) hydrogen bonds : bond 0.04676 / 3.16 ( 967) hydrogen bonds : angle 4.82616 / 3.51 ( 3093) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.391 Fit side-chains REVERT: A 183 ASP cc_start: 0.6890 (t0) cc_final: 0.6677 (t0) REVERT: A 185 ASP cc_start: 0.8193 (m-30) cc_final: 0.7913 (m-30) REVERT: A 354 ASP cc_start: 0.7713 (m-30) cc_final: 0.7473 (m-30) REVERT: B 183 ASP cc_start: 0.6927 (t0) cc_final: 0.6693 (t0) REVERT: B 185 ASP cc_start: 0.8223 (m-30) cc_final: 0.7900 (m-30) REVERT: C 183 ASP cc_start: 0.6929 (t0) cc_final: 0.6693 (t0) REVERT: C 185 ASP cc_start: 0.8219 (m-30) cc_final: 0.7897 (m-30) REVERT: D 183 ASP cc_start: 0.6861 (t0) cc_final: 0.6644 (t0) REVERT: D 185 ASP cc_start: 0.8192 (m-30) cc_final: 0.7905 (m-30) outliers start: 24 outliers final: 12 residues processed: 176 average time/residue: 0.0828 time to fit residues: 23.9913 Evaluate side-chains 157 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 437 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [34, 60, 47, 24, 59, 72, 65, 9, 143, 25, 104] chunk 34 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 HIS A 461 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 HIS B 461 ASN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 HIS C 461 ASN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 HIS D 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.202743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.158221 restraints weight = 14479.698| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.23 r_work: 0.3600 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13232 Z= 0.193 Angle : 0.553 6.801 17912 Z= 0.305 Chirality : 0.041 0.154 2112 Planarity : 0.003 0.031 2176 Dihedral : 4.487 18.364 1720 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.55 % Allowed : 11.57 % Favored : 85.88 % 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: 1.36 (0.21), residues: 1568 helix: 1.95 (0.16), residues: 1032 sheet: 0.25 (0.35), residues: 224 loop : -2.25 (0.27), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 484 TYR 0.014 0.001 TYR B 264 PHE 0.015 0.002 PHE D 494 TRP 0.003 0.001 TRP C 205 HIS 0.006 0.001 HIS B 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (13232) covalent geometry : angle 0.55331 / 0.30 (17912) hydrogen bonds : bond 0.04533 / 3.08 ( 967) hydrogen bonds : angle 4.60594 / 3.34 ( 3093) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.415 Fit side-chains REVERT: A 183 ASP cc_start: 0.7029 (t0) cc_final: 0.6825 (t0) REVERT: A 185 ASP cc_start: 0.8182 (m-30) cc_final: 0.7976 (m-30) REVERT: A 354 ASP cc_start: 0.7662 (m-30) cc_final: 0.7423 (m-30) REVERT: A 380 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7918 (mp) REVERT: B 183 ASP cc_start: 0.7099 (t0) cc_final: 0.6862 (t0) REVERT: B 185 ASP cc_start: 0.8206 (m-30) cc_final: 0.7905 (m-30) REVERT: B 354 ASP cc_start: 0.7764 (m-30) cc_final: 0.7496 (m-30) REVERT: B 380 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7925 (mp) REVERT: C 183 ASP cc_start: 0.7097 (t0) cc_final: 0.6854 (t0) REVERT: C 185 ASP cc_start: 0.8225 (m-30) cc_final: 0.7924 (m-30) REVERT: C 354 ASP cc_start: 0.7767 (m-30) cc_final: 0.7503 (m-30) REVERT: C 380 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7913 (mp) REVERT: D 183 ASP cc_start: 0.7028 (t0) cc_final: 0.6817 (t0) REVERT: D 185 ASP cc_start: 0.8200 (m-30) cc_final: 0.7990 (m-30) REVERT: D 354 ASP cc_start: 0.7751 (m-30) cc_final: 0.7491 (m-30) REVERT: D 380 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7932 (mp) outliers start: 37 outliers final: 22 residues processed: 186 average time/residue: 0.0771 time to fit residues: 23.8263 Evaluate side-chains 186 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 437 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [106, 79, 23, 48, 141, 118, 76, 120, 156, 8, 113] chunk 106 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 141 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 76 optimal weight: 0.2980 chunk 120 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 113 optimal weight: 0.8980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 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 = 0.4347 r_free = 0.4347 target = 0.208454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.164469 restraints weight = 14455.730| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.28 r_work: 0.3673 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13232 Z= 0.117 Angle : 0.472 5.413 17912 Z= 0.262 Chirality : 0.039 0.160 2112 Planarity : 0.003 0.034 2176 Dihedral : 4.227 19.443 1720 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.20 % Allowed : 13.29 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.21), residues: 1568 helix: 2.19 (0.16), residues: 1032 sheet: 0.41 (0.35), residues: 224 loop : -2.25 (0.28), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 212 TYR 0.008 0.001 TYR B 264 PHE 0.011 0.001 PHE A 482 TRP 0.005 0.001 TRP A 480 HIS 0.002 0.000 HIS C 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (13232) covalent geometry : angle 0.47188 / 0.26 (17912) hydrogen bonds : bond 0.03843 / 2.60 ( 967) hydrogen bonds : angle 4.28216 / 3.11 ( 3093) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.496 Fit side-chains REVERT: A 183 ASP cc_start: 0.6992 (t0) cc_final: 0.6754 (t0) REVERT: A 185 ASP cc_start: 0.8257 (m-30) cc_final: 0.8051 (m-30) REVERT: A 380 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7823 (mp) REVERT: B 183 ASP cc_start: 0.7070 (t0) cc_final: 0.6804 (t0) REVERT: B 185 ASP cc_start: 0.8231 (m-30) cc_final: 0.7946 (m-30) REVERT: B 354 ASP cc_start: 0.7667 (m-30) cc_final: 0.7418 (m-30) REVERT: B 380 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7830 (mp) REVERT: C 183 ASP cc_start: 0.7087 (t0) cc_final: 0.6819 (t0) REVERT: C 185 ASP cc_start: 0.8251 (m-30) cc_final: 0.7953 (m-30) REVERT: C 354 ASP cc_start: 0.7683 (m-30) cc_final: 0.7439 (m-30) REVERT: D 354 ASP cc_start: 0.7668 (m-30) cc_final: 0.7423 (m-30) REVERT: D 380 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7828 (mp) outliers start: 32 outliers final: 13 residues processed: 185 average time/residue: 0.0779 time to fit residues: 23.7730 Evaluate side-chains 159 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 437 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [106, 32, 99, 149, 56, 133, 125, 157, 9, 146, 21] chunk 106 optimal weight: 0.0570 chunk 32 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.206423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.162311 restraints weight = 14520.332| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.24 r_work: 0.3662 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13232 Z= 0.153 Angle : 0.510 5.600 17912 Z= 0.280 Chirality : 0.039 0.144 2112 Planarity : 0.003 0.034 2176 Dihedral : 4.319 19.246 1720 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.24 % Allowed : 13.57 % Favored : 83.20 % 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: 1.66 (0.21), residues: 1568 helix: 2.17 (0.16), residues: 1032 sheet: 0.44 (0.34), residues: 224 loop : -2.19 (0.28), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 212 TYR 0.014 0.001 TYR A 264 PHE 0.014 0.002 PHE D 494 TRP 0.004 0.001 TRP A 205 HIS 0.003 0.001 HIS D 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (13232) covalent geometry : angle 0.51030 / 0.28 (17912) hydrogen bonds : bond 0.04080 / 2.76 ( 967) hydrogen bonds : angle 4.30349 / 3.12 ( 3093) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.331 Fit side-chains REVERT: B 185 ASP cc_start: 0.8225 (m-30) cc_final: 0.7974 (m-30) REVERT: B 354 ASP cc_start: 0.7638 (m-30) cc_final: 0.7360 (m-30) REVERT: C 185 ASP cc_start: 0.8250 (m-30) cc_final: 0.7994 (m-30) REVERT: C 354 ASP cc_start: 0.7646 (m-30) cc_final: 0.7368 (m-30) REVERT: C 380 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7950 (mp) REVERT: D 354 ASP cc_start: 0.7641 (m-30) cc_final: 0.7366 (m-30) outliers start: 47 outliers final: 33 residues processed: 199 average time/residue: 0.0727 time to fit residues: 23.5161 Evaluate side-chains 190 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 437 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [76, 5, 60, 158, 151, 85, 46, 29, 57, 88, 143] chunk 76 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 158 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.206733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.163602 restraints weight = 14303.856| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.13 r_work: 0.3663 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13232 Z= 0.147 Angle : 0.513 5.854 17912 Z= 0.280 Chirality : 0.039 0.141 2112 Planarity : 0.003 0.035 2176 Dihedral : 4.323 20.015 1720 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.89 % Allowed : 14.26 % Favored : 82.85 % 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: 1.64 (0.21), residues: 1568 helix: 2.15 (0.16), residues: 1032 sheet: 0.51 (0.34), residues: 224 loop : -2.24 (0.28), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 212 TYR 0.012 0.001 TYR C 264 PHE 0.013 0.001 PHE D 494 TRP 0.004 0.001 TRP C 205 HIS 0.003 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (13232) covalent geometry : angle 0.51308 / 0.28 (17912) hydrogen bonds : bond 0.04026 / 2.72 ( 967) hydrogen bonds : angle 4.28755 / 3.10 ( 3093) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.404 Fit side-chains REVERT: A 380 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7933 (mp) REVERT: B 183 ASP cc_start: 0.6662 (t0) cc_final: 0.6420 (t0) REVERT: B 185 ASP cc_start: 0.8273 (m-30) cc_final: 0.8069 (m-30) REVERT: B 354 ASP cc_start: 0.7642 (m-30) cc_final: 0.7375 (m-30) REVERT: B 380 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7940 (mp) REVERT: C 183 ASP cc_start: 0.6681 (t0) cc_final: 0.6433 (t0) REVERT: C 185 ASP cc_start: 0.8278 (m-30) cc_final: 0.8068 (m-30) REVERT: C 354 ASP cc_start: 0.7659 (m-30) cc_final: 0.7397 (m-30) REVERT: C 380 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7954 (mp) REVERT: D 354 ASP cc_start: 0.7634 (m-30) cc_final: 0.7371 (m-30) REVERT: D 380 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7939 (mp) outliers start: 42 outliers final: 33 residues processed: 193 average time/residue: 0.0820 time to fit residues: 25.9951 Evaluate side-chains 192 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [109, 32, 17, 31, 16, 84, 152, 82, 112, 127, 91] chunk 109 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.210240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.168740 restraints weight = 14309.950| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.11 r_work: 0.3699 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13232 Z= 0.124 Angle : 0.491 7.219 17912 Z= 0.271 Chirality : 0.039 0.164 2112 Planarity : 0.003 0.036 2176 Dihedral : 4.235 20.126 1720 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.48 % Allowed : 13.84 % Favored : 83.68 % 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: 1.81 (0.21), residues: 1568 helix: 2.28 (0.16), residues: 1032 sheet: 0.46 (0.33), residues: 228 loop : -2.13 (0.29), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 139 TYR 0.010 0.001 TYR A 264 PHE 0.024 0.001 PHE A 293 TRP 0.004 0.001 TRP A 480 HIS 0.002 0.001 HIS D 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (13232) covalent geometry : angle 0.49084 / 0.27 (17912) hydrogen bonds : bond 0.03837 / 2.59 ( 967) hydrogen bonds : angle 4.22086 / 3.06 ( 3093) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.545 Fit side-chains REVERT: A 380 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7916 (mp) REVERT: B 183 ASP cc_start: 0.6728 (t0) cc_final: 0.6507 (t0) REVERT: B 185 ASP cc_start: 0.8265 (m-30) cc_final: 0.8051 (m-30) REVERT: B 380 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7927 (mp) REVERT: C 183 ASP cc_start: 0.6759 (t0) cc_final: 0.6533 (t0) REVERT: C 185 ASP cc_start: 0.8278 (m-30) cc_final: 0.8059 (m-30) REVERT: C 380 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7912 (mp) REVERT: D 380 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7928 (mp) outliers start: 36 outliers final: 31 residues processed: 186 average time/residue: 0.0795 time to fit residues: 24.5301 Evaluate side-chains 179 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 380 ILE Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [78, 0, 124, 157, 11, 61, 141, 95, 44, 64, 106] chunk 78 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.210009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.168344 restraints weight = 14246.444| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.04 r_work: 0.3706 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13232 Z= 0.124 Angle : 0.485 6.249 17912 Z= 0.267 Chirality : 0.038 0.135 2112 Planarity : 0.003 0.036 2176 Dihedral : 4.226 19.936 1720 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.89 % Allowed : 14.39 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.21), residues: 1568 helix: 2.26 (0.16), residues: 1032 sheet: 0.44 (0.33), residues: 228 loop : -2.07 (0.29), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 212 TYR 0.011 0.001 TYR C 264 PHE 0.019 0.001 PHE C 293 TRP 0.004 0.001 TRP B 205 HIS 0.002 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13232) covalent geometry : angle 0.48528 / 0.27 (17912) hydrogen bonds : bond 0.03809 / 2.57 ( 967) hydrogen bonds : angle 4.20084 / 3.04 ( 3093) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.465 Fit side-chains outliers start: 42 outliers final: 37 residues processed: 185 average time/residue: 0.0809 time to fit residues: 24.4075 Evaluate side-chains 175 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 378 CYS Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [78, 47, 131, 60, 24, 70, 82, 83, 135, 77, 111] chunk 78 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.210801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.168709 restraints weight = 14314.965| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.05 r_work: 0.3731 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13232 Z= 0.124 Angle : 0.494 6.518 17912 Z= 0.274 Chirality : 0.038 0.137 2112 Planarity : 0.003 0.034 2176 Dihedral : 4.258 19.884 1720 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.27 % Allowed : 14.60 % Favored : 83.13 % 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: 1.82 (0.21), residues: 1568 helix: 2.24 (0.16), residues: 1036 sheet: 0.42 (0.33), residues: 228 loop : -1.93 (0.30), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 484 TYR 0.011 0.001 TYR B 264 PHE 0.017 0.001 PHE C 482 TRP 0.005 0.001 TRP B 436 HIS 0.002 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (13232) covalent geometry : angle 0.49443 / 0.27 (17912) hydrogen bonds : bond 0.03799 / 2.55 ( 967) hydrogen bonds : angle 4.22798 / 3.04 ( 3093) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.488 Fit side-chains outliers start: 33 outliers final: 33 residues processed: 163 average time/residue: 0.0812 time to fit residues: 21.8692 Evaluate side-chains 160 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 378 CYS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [115, 106, 84, 33, 114, 152, 80, 68, 14, 123, 118] chunk 115 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 152 optimal weight: 0.7980 chunk 80 optimal weight: 10.9990 chunk 68 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.210454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.168328 restraints weight = 14345.290| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.05 r_work: 0.3734 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13232 Z= 0.129 Angle : 0.519 8.517 17912 Z= 0.285 Chirality : 0.039 0.157 2112 Planarity : 0.003 0.035 2176 Dihedral : 4.254 19.904 1720 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.13 % Allowed : 14.81 % Favored : 83.06 % 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: 1.82 (0.21), residues: 1568 helix: 2.24 (0.16), residues: 1036 sheet: 0.38 (0.33), residues: 228 loop : -1.89 (0.30), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 484 TYR 0.012 0.001 TYR B 264 PHE 0.016 0.001 PHE C 482 TRP 0.004 0.001 TRP A 205 HIS 0.003 0.001 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (13232) covalent geometry : angle 0.51929 / 0.28 (17912) hydrogen bonds : bond 0.03816 / 2.57 ( 967) hydrogen bonds : angle 4.25506 / 3.07 ( 3093) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.297 Fit side-chains REVERT: C 471 GLN cc_start: 0.7484 (mp10) cc_final: 0.7123 (mp10) REVERT: D 471 GLN cc_start: 0.7473 (mp10) cc_final: 0.7115 (mp10) outliers start: 31 outliers final: 31 residues processed: 155 average time/residue: 0.0809 time to fit residues: 20.5072 Evaluate side-chains 159 residues out of total 1452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 423 CYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 393 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [36, 44, 75, 153, 79, 30, 45, 52, 22, 102, 110] chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 0.0670 chunk 22 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 GLN B 207 GLN D 207 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.212239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.170301 restraints weight = 14297.249| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.06 r_work: 0.3752 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13232 Z= 0.119 Angle : 0.501 8.875 17912 Z= 0.272 Chirality : 0.038 0.158 2112 Planarity : 0.003 0.035 2176 Dihedral : 4.200 19.723 1720 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.20 % Allowed : 15.01 % Favored : 82.78 % 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: 1.86 (0.21), residues: 1568 helix: 2.27 (0.16), residues: 1036 sheet: 0.40 (0.33), residues: 228 loop : -1.88 (0.30), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 212 TYR 0.010 0.001 TYR B 264 PHE 0.013 0.001 PHE D 482 TRP 0.004 0.001 TRP A 205 HIS 0.002 0.000 HIS B 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13232) covalent geometry : angle 0.50058 / 0.27 (17912) hydrogen bonds : bond 0.03716 / 2.51 ( 967) hydrogen bonds : angle 4.23002 / 3.05 ( 3093) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2549.53 seconds wall clock time: 44 minutes 41.99 seconds (2681.99 seconds total)