Starting phenix.real_space_refine on Fri Dec 27 08:07:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eqt_28545/12_2024/8eqt_28545_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eqt_28545/12_2024/8eqt_28545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eqt_28545/12_2024/8eqt_28545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eqt_28545/12_2024/8eqt_28545.map" model { file = "/net/cci-nas-00/data/ceres_data/8eqt_28545/12_2024/8eqt_28545_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eqt_28545/12_2024/8eqt_28545_neut.cif" } resolution = 3.4 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 16 5.16 5 C 2122 2.51 5 N 490 2.21 5 O 574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3206 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1562 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1562 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Time building chain proxies: 2.89, per 1000 atoms: 0.90 Number of scatterers: 3206 At special positions: 0 Unit cell: (63.3, 59.924, 91.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 4 15.00 O 574 8.00 N 490 7.00 C 2122 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: 0.91 Conformation dependent library (CDL) restraints added in 370.7 milliseconds 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 728 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 2 sheets defined 49.7% alpha, 20.9% 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 43 through 61 Processing helix chain 'A' and resid 67 through 100 removed outlier: 4.095A pdb=" N SER A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 134 Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.567A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'B' and resid 43 through 61 Processing helix chain 'B' and resid 67 through 100 removed outlier: 4.095A pdb=" N SER B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 134 Processing helix chain 'B' and resid 136 through 141 removed outlier: 3.567A pdb=" N LEU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 155 through 160 removed outlier: 6.214A pdb=" N HIS A 150 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N CYS A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE A 232 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR A 217 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE A 230 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 155 through 160 removed outlier: 6.214A pdb=" N HIS B 150 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N CYS B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE B 232 " --> pdb=" O TYR B 215 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 217 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE B 230 " --> pdb=" O THR B 217 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 464 1.31 - 1.44: 1042 1.44 - 1.57: 1764 1.57 - 1.69: 8 1.69 - 1.82: 18 Bond restraints: 3296 Sorted by residual: bond pdb=" C10 PEE B 402 " pdb=" O2 PEE B 402 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C10 PEE A 402 " pdb=" O2 PEE A 402 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C30 PEE B 402 " pdb=" O3 PEE B 402 " ideal model delta sigma weight residual 1.327 1.410 -0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 3291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 4442 3.47 - 6.94: 30 6.94 - 10.42: 10 10.42 - 13.89: 2 13.89 - 17.36: 4 Bond angle restraints: 4488 Sorted by residual: angle pdb=" O3P PEE A 401 " pdb=" P PEE A 401 " pdb=" O4P PEE A 401 " ideal model delta sigma weight residual 92.91 110.27 -17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" O3P PEE B 402 " pdb=" P PEE B 402 " pdb=" O4P PEE B 402 " ideal model delta sigma weight residual 92.91 110.27 -17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" O3P PEE B 401 " pdb=" P PEE B 401 " pdb=" O4P PEE B 401 " ideal model delta sigma weight residual 92.91 109.90 -16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" O3P PEE A 402 " pdb=" P PEE A 402 " pdb=" O4P PEE A 402 " ideal model delta sigma weight residual 92.91 109.90 -16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" O1P PEE A 401 " pdb=" P PEE A 401 " pdb=" O2P PEE A 401 " ideal model delta sigma weight residual 119.43 108.94 10.49 3.00e+00 1.11e-01 1.22e+01 ... (remaining 4483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.38: 1822 29.38 - 58.76: 34 58.76 - 88.14: 10 88.14 - 117.52: 6 117.52 - 146.90: 6 Dihedral angle restraints: 1878 sinusoidal: 740 harmonic: 1138 Sorted by residual: dihedral pdb=" C4 PEE A 401 " pdb=" O4P PEE A 401 " pdb=" P PEE A 401 " pdb=" O2P PEE A 401 " ideal model delta sinusoidal sigma weight residual -75.78 71.12 -146.90 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C4 PEE B 402 " pdb=" O4P PEE B 402 " pdb=" P PEE B 402 " pdb=" O2P PEE B 402 " ideal model delta sinusoidal sigma weight residual -75.78 71.12 -146.90 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C3 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C2 PEE B 401 " pdb=" O3P PEE B 401 " ideal model delta sinusoidal sigma weight residual 62.73 -79.00 141.73 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 1875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 446 0.065 - 0.129: 54 0.129 - 0.193: 0 0.193 - 0.258: 0 0.258 - 0.322: 4 Chirality restraints: 504 Sorted by residual: chirality pdb=" C2 PEE B 402 " pdb=" C1 PEE B 402 " pdb=" C3 PEE B 402 " pdb=" O2 PEE B 402 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C3 PEE A 401 " pdb=" O2 PEE A 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C3 PEE B 401 " pdb=" O2 PEE B 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.64 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 501 not shown) Planarity restraints: 530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 79 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.78e+00 pdb=" C PHE B 79 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE B 79 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL B 80 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 79 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.78e+00 pdb=" C PHE A 79 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE A 79 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL A 80 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 87 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" C PHE A 87 " -0.021 2.00e-02 2.50e+03 pdb=" O PHE A 87 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL A 88 " 0.007 2.00e-02 2.50e+03 ... (remaining 527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 339 2.75 - 3.29: 3168 3.29 - 3.83: 5423 3.83 - 4.36: 6176 4.36 - 4.90: 10490 Nonbonded interactions: 25596 Sorted by model distance: nonbonded pdb=" O THR B 89 " pdb=" OG SER B 92 " model vdw 2.213 3.040 nonbonded pdb=" O THR A 89 " pdb=" OG SER A 92 " model vdw 2.213 3.040 nonbonded pdb=" O PRO B 42 " pdb=" OH TYR B 91 " model vdw 2.232 3.040 nonbonded pdb=" O PRO A 42 " pdb=" OH TYR A 91 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR A 151 " pdb=" O TYR A 154 " model vdw 2.248 3.040 ... (remaining 25591 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 40 through 238 or (resid 401 through 402 and (name N or na \ me C1 or name C10 or name C11 or name C2 or name C3 or name C30 or name C31 or n \ ame C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name O3P or n \ ame O4 or name O4P or name O5 or name P )))) selection = (chain 'B' and (resid 40 through 238 or (resid 401 through 402 and (name N or na \ me C1 or name C10 or name C11 or name C2 or name C3 or name C30 or name C31 or n \ ame C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name O3P or n \ ame O4 or name O4P or name O5 or name P )))) } 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: 0.730 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.490 Find NCS groups from input model: 0.100 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.006 0.091 3296 Z= 0.426 Angle : 0.888 17.361 4488 Z= 0.355 Chirality : 0.046 0.322 504 Planarity : 0.004 0.026 530 Dihedral : 17.012 146.900 1150 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.61 (0.40), residues: 374 helix: 1.18 (0.37), residues: 164 sheet: 0.65 (0.56), residues: 90 loop : -0.77 (0.48), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.003 0.001 HIS A 204 PHE 0.005 0.001 PHE B 114 TYR 0.006 0.001 TYR B 156 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.333 Fit side-chains REVERT: A 89 THR cc_start: 0.9351 (m) cc_final: 0.9042 (p) REVERT: A 105 PHE cc_start: 0.9339 (m-80) cc_final: 0.9061 (m-80) REVERT: A 106 LEU cc_start: 0.8382 (pp) cc_final: 0.8128 (tp) REVERT: A 134 ARG cc_start: 0.8323 (tpt170) cc_final: 0.6923 (ttt180) REVERT: A 136 LYS cc_start: 0.8499 (pttt) cc_final: 0.8201 (pttt) REVERT: A 154 TYR cc_start: 0.8408 (t80) cc_final: 0.7536 (t80) REVERT: A 183 ASP cc_start: 0.9086 (p0) cc_final: 0.8709 (p0) REVERT: B 89 THR cc_start: 0.9350 (m) cc_final: 0.9042 (p) REVERT: B 105 PHE cc_start: 0.9337 (m-80) cc_final: 0.9058 (m-80) REVERT: B 106 LEU cc_start: 0.8384 (pp) cc_final: 0.8127 (tp) REVERT: B 134 ARG cc_start: 0.8321 (tpt170) cc_final: 0.6922 (ttt180) REVERT: B 136 LYS cc_start: 0.8499 (pttt) cc_final: 0.8199 (pttt) REVERT: B 154 TYR cc_start: 0.8403 (t80) cc_final: 0.7533 (t80) REVERT: B 183 ASP cc_start: 0.9088 (p0) cc_final: 0.8717 (p0) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1538 time to fit residues: 32.4224 Evaluate side-chains 82 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN B 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3296 Z= 0.207 Angle : 0.505 4.202 4488 Z= 0.264 Chirality : 0.040 0.135 504 Planarity : 0.003 0.022 530 Dihedral : 17.711 144.667 480 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.05 % Allowed : 16.18 % Favored : 79.77 % 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: 1.73 (0.41), residues: 374 helix: 2.71 (0.37), residues: 168 sheet: 0.69 (0.56), residues: 90 loop : -0.88 (0.47), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 193 HIS 0.004 0.001 HIS A 78 PHE 0.025 0.002 PHE A 230 TYR 0.007 0.001 TYR A 113 ARG 0.001 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.310 Fit side-chains REVERT: A 102 GLU cc_start: 0.8602 (mp0) cc_final: 0.8131 (mp0) REVERT: A 106 LEU cc_start: 0.8419 (pp) cc_final: 0.8218 (tp) REVERT: A 134 ARG cc_start: 0.7926 (tpt170) cc_final: 0.7509 (ttt180) REVERT: A 154 TYR cc_start: 0.8396 (t80) cc_final: 0.7686 (t80) REVERT: A 194 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8254 (mt-10) REVERT: A 198 LYS cc_start: 0.8499 (mtmt) cc_final: 0.8060 (mtmt) REVERT: A 213 GLN cc_start: 0.9142 (tt0) cc_final: 0.8941 (tt0) REVERT: A 216 SER cc_start: 0.8858 (t) cc_final: 0.8636 (t) REVERT: A 233 TYR cc_start: 0.9490 (m-80) cc_final: 0.8807 (m-80) REVERT: B 102 GLU cc_start: 0.8594 (mp0) cc_final: 0.8124 (mp0) REVERT: B 106 LEU cc_start: 0.8421 (pp) cc_final: 0.8218 (tp) REVERT: B 134 ARG cc_start: 0.7926 (tpt170) cc_final: 0.7508 (ttt180) REVERT: B 154 TYR cc_start: 0.8396 (t80) cc_final: 0.7684 (t80) REVERT: B 194 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8266 (mt-10) REVERT: B 198 LYS cc_start: 0.8499 (mtmt) cc_final: 0.8057 (mtmt) REVERT: B 213 GLN cc_start: 0.9144 (tt0) cc_final: 0.8943 (tt0) REVERT: B 216 SER cc_start: 0.8855 (t) cc_final: 0.8633 (t) REVERT: B 233 TYR cc_start: 0.9489 (m-80) cc_final: 0.8788 (m-80) outliers start: 14 outliers final: 12 residues processed: 122 average time/residue: 0.1728 time to fit residues: 24.7947 Evaluate side-chains 108 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 229 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3296 Z= 0.199 Angle : 0.453 4.441 4488 Z= 0.242 Chirality : 0.040 0.131 504 Planarity : 0.003 0.021 530 Dihedral : 16.737 143.599 480 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.05 % Allowed : 19.65 % Favored : 76.30 % 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: 1.75 (0.41), residues: 374 helix: 2.82 (0.37), residues: 168 sheet: 0.76 (0.58), residues: 86 loop : -1.04 (0.44), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.003 0.001 HIS B 227 PHE 0.014 0.002 PHE B 43 TYR 0.006 0.001 TYR B 109 ARG 0.000 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8509 (mp0) cc_final: 0.8247 (mp0) REVERT: A 105 PHE cc_start: 0.9344 (m-80) cc_final: 0.9091 (m-80) REVERT: A 134 ARG cc_start: 0.8069 (tpt170) cc_final: 0.7553 (ttt180) REVERT: A 136 LYS cc_start: 0.8625 (pttt) cc_final: 0.8336 (pttt) REVERT: A 155 ASP cc_start: 0.7748 (p0) cc_final: 0.7242 (p0) REVERT: A 194 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8297 (mt-10) REVERT: A 213 GLN cc_start: 0.9134 (tt0) cc_final: 0.8910 (tt0) REVERT: A 216 SER cc_start: 0.8978 (t) cc_final: 0.8763 (t) REVERT: A 232 ILE cc_start: 0.9020 (mm) cc_final: 0.8729 (mm) REVERT: B 102 GLU cc_start: 0.8506 (mp0) cc_final: 0.8242 (mp0) REVERT: B 105 PHE cc_start: 0.9342 (m-80) cc_final: 0.9087 (m-80) REVERT: B 134 ARG cc_start: 0.8066 (tpt170) cc_final: 0.7552 (ttt180) REVERT: B 136 LYS cc_start: 0.8621 (pttt) cc_final: 0.8331 (pttt) REVERT: B 155 ASP cc_start: 0.7747 (p0) cc_final: 0.7243 (p0) REVERT: B 194 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8306 (mt-10) REVERT: B 213 GLN cc_start: 0.9137 (tt0) cc_final: 0.8913 (tt0) REVERT: B 216 SER cc_start: 0.8971 (t) cc_final: 0.8760 (t) REVERT: B 232 ILE cc_start: 0.9010 (mm) cc_final: 0.8722 (mm) outliers start: 14 outliers final: 14 residues processed: 126 average time/residue: 0.1527 time to fit residues: 23.1772 Evaluate side-chains 122 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS A 204 HIS A 227 HIS B 182 HIS B 204 HIS B 227 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3296 Z= 0.197 Angle : 0.466 5.225 4488 Z= 0.250 Chirality : 0.039 0.138 504 Planarity : 0.003 0.020 530 Dihedral : 16.336 144.458 480 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.62 % Allowed : 23.12 % Favored : 72.25 % 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: 1.75 (0.41), residues: 374 helix: 2.70 (0.36), residues: 180 sheet: 0.78 (0.56), residues: 84 loop : -1.23 (0.48), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.003 0.001 HIS B 204 PHE 0.017 0.002 PHE A 114 TYR 0.005 0.001 TYR B 160 ARG 0.001 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.473 Fit side-chains REVERT: A 102 GLU cc_start: 0.8365 (mp0) cc_final: 0.8082 (mp0) REVERT: A 134 ARG cc_start: 0.8037 (tpt170) cc_final: 0.7510 (ttt180) REVERT: A 136 LYS cc_start: 0.8656 (pttt) cc_final: 0.8328 (pttt) REVERT: A 154 TYR cc_start: 0.8373 (t80) cc_final: 0.8085 (t80) REVERT: A 155 ASP cc_start: 0.7719 (p0) cc_final: 0.7161 (p0) REVERT: A 194 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8270 (mt-10) REVERT: A 198 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8315 (mtmt) REVERT: A 211 TYR cc_start: 0.7914 (m-80) cc_final: 0.7655 (m-80) REVERT: A 216 SER cc_start: 0.9009 (t) cc_final: 0.8770 (t) REVERT: A 226 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7666 (tm-30) REVERT: A 227 HIS cc_start: 0.8459 (OUTLIER) cc_final: 0.7542 (m90) REVERT: B 102 GLU cc_start: 0.8358 (mp0) cc_final: 0.8075 (mp0) REVERT: B 134 ARG cc_start: 0.8036 (tpt170) cc_final: 0.7511 (ttt180) REVERT: B 136 LYS cc_start: 0.8653 (pttt) cc_final: 0.8324 (pttt) REVERT: B 154 TYR cc_start: 0.8371 (t80) cc_final: 0.8086 (t80) REVERT: B 155 ASP cc_start: 0.7717 (p0) cc_final: 0.7158 (p0) REVERT: B 194 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8279 (mt-10) REVERT: B 198 LYS cc_start: 0.8654 (mtmt) cc_final: 0.8312 (mtmt) REVERT: B 211 TYR cc_start: 0.7915 (m-80) cc_final: 0.7655 (m-80) REVERT: B 216 SER cc_start: 0.9000 (t) cc_final: 0.8757 (t) REVERT: B 226 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7730 (tm-30) REVERT: B 227 HIS cc_start: 0.8429 (OUTLIER) cc_final: 0.7531 (m90) outliers start: 16 outliers final: 12 residues processed: 103 average time/residue: 0.1731 time to fit residues: 21.1569 Evaluate side-chains 98 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 227 HIS B 70 GLN B 227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3296 Z= 0.163 Angle : 0.432 4.538 4488 Z= 0.235 Chirality : 0.039 0.136 504 Planarity : 0.003 0.020 530 Dihedral : 15.959 139.063 480 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.89 % Allowed : 26.59 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.82 (0.42), residues: 374 helix: 2.67 (0.35), residues: 192 sheet: 0.69 (0.55), residues: 84 loop : -1.40 (0.49), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 128 HIS 0.007 0.001 HIS A 227 PHE 0.018 0.002 PHE B 114 TYR 0.005 0.001 TYR B 109 ARG 0.001 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8390 (mp0) cc_final: 0.8068 (mp0) REVERT: A 134 ARG cc_start: 0.8112 (tpt170) cc_final: 0.7608 (ttt180) REVERT: A 136 LYS cc_start: 0.8642 (pttt) cc_final: 0.8307 (pttt) REVERT: A 154 TYR cc_start: 0.8346 (t80) cc_final: 0.8042 (t80) REVERT: A 155 ASP cc_start: 0.7772 (p0) cc_final: 0.7211 (p0) REVERT: A 194 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8244 (mt-10) REVERT: A 211 TYR cc_start: 0.7937 (m-80) cc_final: 0.7705 (m-80) REVERT: A 216 SER cc_start: 0.8997 (t) cc_final: 0.8777 (t) REVERT: B 102 GLU cc_start: 0.8385 (mp0) cc_final: 0.8060 (mp0) REVERT: B 134 ARG cc_start: 0.8113 (tpt170) cc_final: 0.7607 (ttt180) REVERT: B 136 LYS cc_start: 0.8639 (pttt) cc_final: 0.8303 (pttt) REVERT: B 154 TYR cc_start: 0.8342 (t80) cc_final: 0.8041 (t80) REVERT: B 155 ASP cc_start: 0.7776 (p0) cc_final: 0.7209 (p0) REVERT: B 194 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8254 (mt-10) REVERT: B 211 TYR cc_start: 0.7936 (m-80) cc_final: 0.7705 (m-80) REVERT: B 216 SER cc_start: 0.8987 (t) cc_final: 0.8764 (t) REVERT: B 226 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7596 (tm-30) REVERT: B 227 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.7600 (m90) outliers start: 10 outliers final: 9 residues processed: 96 average time/residue: 0.1807 time to fit residues: 20.5312 Evaluate side-chains 94 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.0670 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS B 227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3296 Z= 0.178 Angle : 0.418 4.611 4488 Z= 0.229 Chirality : 0.039 0.136 504 Planarity : 0.003 0.019 530 Dihedral : 15.776 135.466 480 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.62 % Allowed : 23.12 % Favored : 72.25 % 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: 1.91 (0.42), residues: 374 helix: 2.84 (0.36), residues: 192 sheet: 0.59 (0.53), residues: 84 loop : -1.44 (0.50), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.008 0.001 HIS A 227 PHE 0.023 0.002 PHE A 114 TYR 0.005 0.001 TYR B 160 ARG 0.001 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8084 (tpt170) cc_final: 0.7673 (ttt180) REVERT: A 154 TYR cc_start: 0.8324 (t80) cc_final: 0.8008 (t80) REVERT: A 155 ASP cc_start: 0.7846 (p0) cc_final: 0.7264 (p0) REVERT: A 194 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8242 (mt-10) REVERT: A 211 TYR cc_start: 0.7974 (m-80) cc_final: 0.7757 (m-80) REVERT: A 216 SER cc_start: 0.9007 (t) cc_final: 0.8778 (t) REVERT: B 134 ARG cc_start: 0.8082 (tpt170) cc_final: 0.7672 (ttt180) REVERT: B 154 TYR cc_start: 0.8321 (t80) cc_final: 0.8007 (t80) REVERT: B 155 ASP cc_start: 0.7847 (p0) cc_final: 0.7270 (p0) REVERT: B 194 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8253 (mt-10) REVERT: B 211 TYR cc_start: 0.7974 (m-80) cc_final: 0.7757 (m-80) REVERT: B 216 SER cc_start: 0.9001 (t) cc_final: 0.8770 (t) outliers start: 16 outliers final: 16 residues processed: 102 average time/residue: 0.1713 time to fit residues: 20.9290 Evaluate side-chains 100 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3296 Z= 0.199 Angle : 0.463 4.735 4488 Z= 0.254 Chirality : 0.039 0.134 504 Planarity : 0.003 0.019 530 Dihedral : 15.753 135.367 480 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.62 % Allowed : 22.54 % Favored : 72.83 % 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: 1.98 (0.43), residues: 374 helix: 2.94 (0.36), residues: 192 sheet: 0.52 (0.53), residues: 84 loop : -1.44 (0.51), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.010 0.001 HIS A 227 PHE 0.026 0.002 PHE B 114 TYR 0.007 0.001 TYR A 109 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.373 Fit side-chains REVERT: A 102 GLU cc_start: 0.8930 (pm20) cc_final: 0.8301 (mp0) REVERT: A 134 ARG cc_start: 0.8105 (tpt170) cc_final: 0.7697 (ttt180) REVERT: A 154 TYR cc_start: 0.8288 (t80) cc_final: 0.7998 (t80) REVERT: A 155 ASP cc_start: 0.7819 (p0) cc_final: 0.7211 (p0) REVERT: A 194 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8241 (mt-10) REVERT: A 198 LYS cc_start: 0.8444 (mtmt) cc_final: 0.7844 (mmtm) REVERT: A 211 TYR cc_start: 0.7988 (m-80) cc_final: 0.7757 (m-80) REVERT: A 216 SER cc_start: 0.9007 (t) cc_final: 0.8776 (t) REVERT: A 226 GLU cc_start: 0.8328 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 227 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.7638 (m-70) REVERT: B 134 ARG cc_start: 0.8104 (tpt170) cc_final: 0.7696 (ttt180) REVERT: B 154 TYR cc_start: 0.8287 (t80) cc_final: 0.7998 (t80) REVERT: B 155 ASP cc_start: 0.7820 (p0) cc_final: 0.7213 (p0) REVERT: B 194 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8244 (mt-10) REVERT: B 198 LYS cc_start: 0.8449 (mtmt) cc_final: 0.7859 (mmtm) REVERT: B 211 TYR cc_start: 0.7986 (m-80) cc_final: 0.7755 (m-80) REVERT: B 216 SER cc_start: 0.9004 (t) cc_final: 0.8770 (t) REVERT: B 226 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7636 (tm-30) REVERT: B 227 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.7495 (m90) outliers start: 16 outliers final: 14 residues processed: 98 average time/residue: 0.1655 time to fit residues: 19.3852 Evaluate side-chains 98 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.0070 chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS B 70 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3296 Z= 0.145 Angle : 0.436 5.034 4488 Z= 0.242 Chirality : 0.039 0.135 504 Planarity : 0.003 0.020 530 Dihedral : 15.418 134.529 480 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.91 % Allowed : 22.54 % Favored : 72.54 % 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: 1.98 (0.43), residues: 374 helix: 2.97 (0.36), residues: 192 sheet: 0.33 (0.54), residues: 86 loop : -1.32 (0.51), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.007 0.001 HIS B 227 PHE 0.023 0.002 PHE B 114 TYR 0.005 0.001 TYR B 109 ARG 0.001 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.635 Fit side-chains REVERT: A 134 ARG cc_start: 0.8157 (tpt170) cc_final: 0.7771 (ttt180) REVERT: A 154 TYR cc_start: 0.8214 (t80) cc_final: 0.7872 (t80) REVERT: A 155 ASP cc_start: 0.7767 (p0) cc_final: 0.7177 (p0) REVERT: A 194 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8236 (mt-10) REVERT: A 198 LYS cc_start: 0.8467 (mtmt) cc_final: 0.7891 (mmtm) REVERT: A 216 SER cc_start: 0.8969 (t) cc_final: 0.8618 (p) REVERT: A 226 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 227 HIS cc_start: 0.8533 (OUTLIER) cc_final: 0.7601 (m90) REVERT: A 234 ASN cc_start: 0.9044 (t0) cc_final: 0.8822 (t0) REVERT: B 134 ARG cc_start: 0.8158 (tpt170) cc_final: 0.7769 (ttt180) REVERT: B 154 TYR cc_start: 0.8209 (t80) cc_final: 0.7897 (t80) REVERT: B 155 ASP cc_start: 0.7772 (p0) cc_final: 0.7179 (p0) REVERT: B 194 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8240 (mt-10) REVERT: B 198 LYS cc_start: 0.8458 (mtmt) cc_final: 0.7932 (mmtm) REVERT: B 216 SER cc_start: 0.8972 (t) cc_final: 0.8622 (p) REVERT: B 234 ASN cc_start: 0.9034 (t0) cc_final: 0.8805 (t0) outliers start: 17 outliers final: 12 residues processed: 106 average time/residue: 0.1647 time to fit residues: 21.1685 Evaluate side-chains 97 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.4980 chunk 3 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS B 227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3296 Z= 0.181 Angle : 0.463 5.945 4488 Z= 0.257 Chirality : 0.039 0.136 504 Planarity : 0.003 0.020 530 Dihedral : 15.299 138.841 480 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.62 % Allowed : 23.70 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.00 (0.42), residues: 374 helix: 2.99 (0.36), residues: 192 sheet: 0.52 (0.53), residues: 84 loop : -1.49 (0.50), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.009 0.001 HIS A 227 PHE 0.026 0.002 PHE A 114 TYR 0.005 0.001 TYR B 109 ARG 0.001 0.000 ARG B 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.353 Fit side-chains REVERT: A 134 ARG cc_start: 0.8135 (tpt170) cc_final: 0.7646 (ttp-170) REVERT: A 154 TYR cc_start: 0.8193 (t80) cc_final: 0.7876 (t80) REVERT: A 155 ASP cc_start: 0.7778 (p0) cc_final: 0.7234 (p0) REVERT: A 194 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8225 (mt-10) REVERT: A 198 LYS cc_start: 0.8446 (mtmt) cc_final: 0.7841 (mmtm) REVERT: A 216 SER cc_start: 0.9016 (t) cc_final: 0.8796 (t) REVERT: A 226 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 227 HIS cc_start: 0.8484 (OUTLIER) cc_final: 0.7427 (m90) REVERT: A 234 ASN cc_start: 0.9098 (t0) cc_final: 0.8866 (t0) REVERT: B 134 ARG cc_start: 0.8133 (tpt170) cc_final: 0.7644 (ttp-170) REVERT: B 154 TYR cc_start: 0.8188 (t80) cc_final: 0.7873 (t80) REVERT: B 155 ASP cc_start: 0.7779 (p0) cc_final: 0.7233 (p0) REVERT: B 194 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8237 (mt-10) REVERT: B 198 LYS cc_start: 0.8544 (mtmt) cc_final: 0.7928 (mmtm) REVERT: B 216 SER cc_start: 0.8972 (t) cc_final: 0.8750 (t) REVERT: B 226 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7642 (tm-30) REVERT: B 227 HIS cc_start: 0.8537 (OUTLIER) cc_final: 0.7474 (m90) outliers start: 16 outliers final: 12 residues processed: 98 average time/residue: 0.1642 time to fit residues: 19.2143 Evaluate side-chains 99 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN B 70 GLN B 227 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3296 Z= 0.185 Angle : 0.461 6.050 4488 Z= 0.255 Chirality : 0.039 0.136 504 Planarity : 0.003 0.021 530 Dihedral : 15.303 142.383 480 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.62 % Allowed : 23.70 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.01 (0.42), residues: 374 helix: 3.02 (0.36), residues: 192 sheet: 0.51 (0.52), residues: 84 loop : -1.53 (0.50), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.005 0.001 HIS A 227 PHE 0.027 0.002 PHE A 114 TYR 0.005 0.001 TYR B 109 ARG 0.001 0.000 ARG B 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 748 Ramachandran restraints generated. 374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.333 Fit side-chains REVERT: A 134 ARG cc_start: 0.8141 (tpt170) cc_final: 0.7651 (ttp-170) REVERT: A 154 TYR cc_start: 0.8186 (t80) cc_final: 0.7874 (t80) REVERT: A 155 ASP cc_start: 0.7780 (p0) cc_final: 0.7234 (p0) REVERT: A 194 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8223 (mt-10) REVERT: A 198 LYS cc_start: 0.8441 (mtmt) cc_final: 0.7918 (mmtm) REVERT: A 216 SER cc_start: 0.9014 (t) cc_final: 0.8795 (t) REVERT: A 226 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7838 (tm-30) REVERT: A 227 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.7662 (m-70) REVERT: A 234 ASN cc_start: 0.9109 (t0) cc_final: 0.8864 (t0) REVERT: B 134 ARG cc_start: 0.8142 (tpt170) cc_final: 0.7647 (ttp-170) REVERT: B 154 TYR cc_start: 0.8182 (t80) cc_final: 0.7867 (t80) REVERT: B 155 ASP cc_start: 0.7775 (p0) cc_final: 0.7225 (p0) REVERT: B 194 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8235 (mt-10) REVERT: B 198 LYS cc_start: 0.8540 (mtmt) cc_final: 0.7877 (mmtm) REVERT: B 216 SER cc_start: 0.8989 (t) cc_final: 0.8760 (t) REVERT: B 226 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7560 (tm-30) REVERT: B 227 HIS cc_start: 0.8567 (OUTLIER) cc_final: 0.7474 (m90) outliers start: 16 outliers final: 12 residues processed: 99 average time/residue: 0.1702 time to fit residues: 20.0193 Evaluate side-chains 99 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 81 CYS Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS B 227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.101538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.076717 restraints weight = 6294.258| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.88 r_work: 0.2804 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3296 Z= 0.196 Angle : 0.470 6.399 4488 Z= 0.259 Chirality : 0.039 0.138 504 Planarity : 0.003 0.019 530 Dihedral : 15.371 146.180 480 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.62 % Allowed : 23.12 % Favored : 72.25 % 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: 2.02 (0.43), residues: 374 helix: 3.03 (0.36), residues: 192 sheet: 0.47 (0.53), residues: 84 loop : -1.47 (0.50), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.004 0.001 HIS A 227 PHE 0.027 0.002 PHE A 114 TYR 0.005 0.001 TYR B 109 ARG 0.001 0.000 ARG B 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1286.77 seconds wall clock time: 24 minutes 13.79 seconds (1453.79 seconds total)