Starting phenix.real_space_refine on Fri May 9 19:13:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eqt_28545/05_2025/8eqt_28545_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eqt_28545/05_2025/8eqt_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_28545/05_2025/8eqt_28545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eqt_28545/05_2025/8eqt_28545.map" model { file = "/net/cci-nas-00/data/ceres_data/8eqt_28545/05_2025/8eqt_28545_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eqt_28545/05_2025/8eqt_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-5687/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: 2.50, per 1000 atoms: 0.78 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: 0.74 Conformation dependent library (CDL) restraints added in 325.7 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: 0.37 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: 0.83 Time building geometry restraints manager: 0.87 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: 0.01 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: 0.720 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.530 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.390 ------------------------------------------------------------------------------- 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= 0.318 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 Details of bonding type rmsd hydrogen bonds : bond 0.12924 ( 204) hydrogen bonds : angle 6.59782 ( 594) covalent geometry : bond 0.00634 ( 3296) covalent geometry : angle 0.88755 ( 4488) *********************** 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 : 0.349 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: 0.1497 time to fit residues: 31.8909 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 : 0.335 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.102078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.077409 restraints weight = 6238.511| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.00 r_work: 0.2828 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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= 0.143 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 Details of bonding type rmsd hydrogen bonds : bond 0.02867 ( 204) hydrogen bonds : angle 4.55270 ( 594) covalent geometry : bond 0.00318 ( 3296) covalent geometry : angle 0.50514 ( 4488) *********************** 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 : 0.324 Fit side-chains REVERT: A 102 GLU cc_start: 0.8527 (mp0) cc_final: 0.8102 (mp0) REVERT: A 106 LEU cc_start: 0.8491 (pp) cc_final: 0.8288 (tp) REVERT: A 134 ARG cc_start: 0.8051 (tpt170) cc_final: 0.7577 (ttt180) REVERT: A 154 TYR cc_start: 0.8432 (t80) cc_final: 0.7753 (t80) REVERT: A 194 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8490 (mt-10) REVERT: A 198 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8162 (mtmt) REVERT: A 233 TYR cc_start: 0.9606 (m-80) cc_final: 0.9007 (m-80) REVERT: B 102 GLU cc_start: 0.8539 (mp0) cc_final: 0.8108 (mp0) REVERT: B 106 LEU cc_start: 0.8488 (pp) cc_final: 0.8286 (tp) REVERT: B 134 ARG cc_start: 0.8060 (tpt170) cc_final: 0.7583 (ttt180) REVERT: B 154 TYR cc_start: 0.8434 (t80) cc_final: 0.7757 (t80) REVERT: B 194 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8466 (mt-10) REVERT: B 198 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8156 (mtmt) REVERT: B 233 TYR cc_start: 0.9607 (m-80) cc_final: 0.8986 (m-80) outliers start: 14 outliers final: 12 residues processed: 122 average time/residue: 0.1687 time to fit residues: 24.1930 Evaluate side-chains 106 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 11 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.098982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.074451 restraints weight = 6301.631| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.97 r_work: 0.2778 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4001 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= 0.142 Angle : 0.459 4.449 4488 Z= 0.245 Chirality : 0.040 0.131 504 Planarity : 0.003 0.021 530 Dihedral : 16.714 144.332 480 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.62 % Allowed : 19.65 % Favored : 75.72 % 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 (0.42), residues: 374 helix: 2.82 (0.37), residues: 168 sheet: 0.76 (0.58), residues: 86 loop : -1.03 (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 A 204 PHE 0.015 0.002 PHE B 43 TYR 0.006 0.001 TYR B 109 ARG 0.000 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.02799 ( 204) hydrogen bonds : angle 4.33212 ( 594) covalent geometry : bond 0.00319 ( 3296) covalent geometry : angle 0.45865 ( 4488) *********************** 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 132 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8408 (mp0) cc_final: 0.8162 (mp0) REVERT: A 105 PHE cc_start: 0.9333 (m-80) cc_final: 0.9092 (m-80) REVERT: A 134 ARG cc_start: 0.8167 (tpt170) cc_final: 0.7622 (ttt180) REVERT: A 136 LYS cc_start: 0.8746 (pttt) cc_final: 0.8466 (pttt) REVERT: A 155 ASP cc_start: 0.7968 (p0) cc_final: 0.7459 (p0) REVERT: A 194 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8500 (mt-10) REVERT: A 232 ILE cc_start: 0.9385 (mm) cc_final: 0.9043 (mm) REVERT: B 102 GLU cc_start: 0.8397 (mp0) cc_final: 0.8143 (mp0) REVERT: B 105 PHE cc_start: 0.9332 (m-80) cc_final: 0.9090 (m-80) REVERT: B 134 ARG cc_start: 0.8172 (tpt170) cc_final: 0.7622 (ttt180) REVERT: B 136 LYS cc_start: 0.8746 (pttt) cc_final: 0.8471 (pttt) REVERT: B 155 ASP cc_start: 0.7967 (p0) cc_final: 0.7469 (p0) REVERT: B 194 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8483 (mt-10) REVERT: B 232 ILE cc_start: 0.9370 (mm) cc_final: 0.9014 (mm) outliers start: 16 outliers final: 14 residues processed: 128 average time/residue: 0.1400 time to fit residues: 21.6861 Evaluate side-chains 120 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 15 optimal weight: 0.0870 chunk 31 optimal weight: 0.0030 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS A 227 HIS B 182 HIS B 227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.076780 restraints weight = 6302.489| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.97 r_work: 0.2827 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3296 Z= 0.108 Angle : 0.453 5.347 4488 Z= 0.244 Chirality : 0.039 0.138 504 Planarity : 0.003 0.021 530 Dihedral : 16.191 142.725 480 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.47 % Allowed : 25.43 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.42), residues: 374 helix: 2.68 (0.36), residues: 180 sheet: 0.64 (0.56), residues: 86 loop : -1.16 (0.48), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.004 0.001 HIS A 227 PHE 0.017 0.002 PHE A 114 TYR 0.004 0.001 TYR B 160 ARG 0.000 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02527 ( 204) hydrogen bonds : angle 4.14358 ( 594) covalent geometry : bond 0.00238 ( 3296) covalent geometry : angle 0.45314 ( 4488) *********************** 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 103 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.365 Fit side-chains REVERT: A 102 GLU cc_start: 0.8316 (mp0) cc_final: 0.8079 (mp0) REVERT: A 105 PHE cc_start: 0.9306 (m-80) cc_final: 0.9088 (m-80) REVERT: A 134 ARG cc_start: 0.8100 (tpt170) cc_final: 0.7595 (ttt180) REVERT: A 136 LYS cc_start: 0.8771 (pttt) cc_final: 0.8462 (pttt) REVERT: A 154 TYR cc_start: 0.8422 (t80) cc_final: 0.8139 (t80) REVERT: A 155 ASP cc_start: 0.7863 (p0) cc_final: 0.7348 (p0) REVERT: A 194 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8457 (mt-10) REVERT: A 198 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8470 (mtmt) REVERT: A 226 GLU cc_start: 0.8630 (tm-30) cc_final: 0.7983 (tm-30) REVERT: A 227 HIS cc_start: 0.8568 (OUTLIER) cc_final: 0.7723 (m90) REVERT: B 102 GLU cc_start: 0.8308 (mp0) cc_final: 0.8066 (mp0) REVERT: B 105 PHE cc_start: 0.9302 (m-80) cc_final: 0.9082 (m-80) REVERT: B 134 ARG cc_start: 0.8118 (tpt170) cc_final: 0.7602 (ttt180) REVERT: B 136 LYS cc_start: 0.8775 (pttt) cc_final: 0.8471 (pttt) REVERT: B 154 TYR cc_start: 0.8427 (t80) cc_final: 0.8150 (t80) REVERT: B 155 ASP cc_start: 0.7872 (p0) cc_final: 0.7376 (p0) REVERT: B 194 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8431 (mt-10) REVERT: B 198 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8455 (mtmt) REVERT: B 211 TYR cc_start: 0.8122 (m-80) cc_final: 0.7904 (m-80) REVERT: B 226 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8068 (tm-30) REVERT: B 227 HIS cc_start: 0.8570 (OUTLIER) cc_final: 0.7740 (m90) outliers start: 12 outliers final: 8 residues processed: 101 average time/residue: 0.1686 time to fit residues: 20.2930 Evaluate side-chains 91 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 127 LEU Chi-restraints excluded: chain A residue 198 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 127 LEU Chi-restraints excluded: chain B residue 198 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 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.0010 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 70 GLN A 204 HIS A 227 HIS B 57 GLN B 70 GLN B 204 HIS B 227 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.099778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.075491 restraints weight = 6178.255| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.78 r_work: 0.2801 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3296 Z= 0.157 Angle : 0.443 4.566 4488 Z= 0.241 Chirality : 0.039 0.136 504 Planarity : 0.003 0.020 530 Dihedral : 15.952 135.222 480 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 5.20 % Allowed : 24.28 % 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: 1.80 (0.41), residues: 374 helix: 2.88 (0.36), residues: 180 sheet: 0.73 (0.54), residues: 84 loop : -1.45 (0.46), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.012 0.002 HIS B 227 PHE 0.021 0.002 PHE B 114 TYR 0.006 0.001 TYR A 109 ARG 0.001 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.02613 ( 204) hydrogen bonds : angle 4.15058 ( 594) covalent geometry : bond 0.00352 ( 3296) covalent geometry : angle 0.44315 ( 4488) *********************** 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 98 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8303 (mp0) cc_final: 0.8020 (mp0) REVERT: A 134 ARG cc_start: 0.8154 (tpt170) cc_final: 0.7714 (ttt180) REVERT: A 154 TYR cc_start: 0.8379 (t80) cc_final: 0.8075 (t80) REVERT: A 155 ASP cc_start: 0.7994 (p0) cc_final: 0.7435 (p0) REVERT: A 194 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8506 (mt-10) REVERT: A 198 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8371 (mtmt) REVERT: A 211 TYR cc_start: 0.8198 (m-80) cc_final: 0.7937 (m-80) REVERT: B 102 GLU cc_start: 0.8291 (mp0) cc_final: 0.7997 (mp0) REVERT: B 134 ARG cc_start: 0.8170 (tpt170) cc_final: 0.7709 (ttt180) REVERT: B 154 TYR cc_start: 0.8388 (t80) cc_final: 0.8088 (t80) REVERT: B 155 ASP cc_start: 0.7995 (p0) cc_final: 0.7441 (p0) REVERT: B 194 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8509 (mt-10) REVERT: B 198 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8369 (mtmt) REVERT: B 211 TYR cc_start: 0.8204 (m-80) cc_final: 0.7943 (m-80) outliers start: 18 outliers final: 12 residues processed: 96 average time/residue: 0.1662 time to fit residues: 19.0185 Evaluate side-chains 92 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.102508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.077400 restraints weight = 6408.408| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.98 r_work: 0.2832 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3296 Z= 0.110 Angle : 0.424 4.513 4488 Z= 0.233 Chirality : 0.039 0.136 504 Planarity : 0.002 0.020 530 Dihedral : 15.670 132.564 480 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.47 % Allowed : 25.72 % Favored : 70.81 % 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: 1.81 (0.41), residues: 374 helix: 2.96 (0.36), residues: 180 sheet: 0.65 (0.54), residues: 84 loop : -1.51 (0.46), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 128 HIS 0.008 0.001 HIS A 227 PHE 0.018 0.002 PHE B 114 TYR 0.004 0.001 TYR A 160 ARG 0.001 0.000 ARG A 122 Details of bonding type rmsd hydrogen bonds : bond 0.02458 ( 204) hydrogen bonds : angle 4.03078 ( 594) covalent geometry : bond 0.00247 ( 3296) covalent geometry : angle 0.42444 ( 4488) *********************** 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 98 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8180 (tpt170) cc_final: 0.7767 (ttt180) REVERT: A 154 TYR cc_start: 0.8307 (t80) cc_final: 0.7990 (t80) REVERT: A 155 ASP cc_start: 0.8007 (p0) cc_final: 0.7451 (p0) REVERT: A 194 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8453 (mt-10) REVERT: A 198 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8389 (mtmt) REVERT: B 102 GLU cc_start: 0.8296 (mp0) cc_final: 0.7997 (mp0) REVERT: B 105 PHE cc_start: 0.9366 (m-80) cc_final: 0.9164 (m-80) REVERT: B 134 ARG cc_start: 0.8199 (tpt170) cc_final: 0.7769 (ttt180) REVERT: B 154 TYR cc_start: 0.8338 (t80) cc_final: 0.8028 (t80) REVERT: B 155 ASP cc_start: 0.8022 (p0) cc_final: 0.7467 (p0) REVERT: B 194 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8458 (mt-10) REVERT: B 198 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8388 (mtmt) REVERT: B 218 GLN cc_start: 0.9182 (mm110) cc_final: 0.8938 (mm110) REVERT: B 226 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8011 (tm-30) REVERT: B 227 HIS cc_start: 0.8635 (OUTLIER) cc_final: 0.7787 (m90) outliers start: 12 outliers final: 11 residues processed: 98 average time/residue: 0.1581 time to fit residues: 18.4976 Evaluate side-chains 91 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 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 34 optimal weight: 0.0060 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.100985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.076407 restraints weight = 6236.724| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.88 r_work: 0.2814 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3296 Z= 0.134 Angle : 0.439 4.999 4488 Z= 0.240 Chirality : 0.039 0.134 504 Planarity : 0.003 0.020 530 Dihedral : 15.573 136.577 480 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 5.78 % Allowed : 23.12 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.79 (0.41), residues: 374 helix: 3.03 (0.36), residues: 180 sheet: 0.49 (0.52), residues: 84 loop : -1.53 (0.47), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 A 160 ARG 0.001 0.000 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.02480 ( 204) hydrogen bonds : angle 4.02436 ( 594) covalent geometry : bond 0.00304 ( 3296) covalent geometry : angle 0.43850 ( 4488) *********************** 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 101 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.367 Fit side-chains REVERT: A 134 ARG cc_start: 0.8196 (tpt170) cc_final: 0.7769 (ttt180) REVERT: A 154 TYR cc_start: 0.8295 (t80) cc_final: 0.7991 (t80) REVERT: A 155 ASP cc_start: 0.7978 (p0) cc_final: 0.7400 (p0) REVERT: A 194 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8453 (mt-10) REVERT: A 198 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8420 (mtmt) REVERT: A 226 GLU cc_start: 0.8631 (tm-30) cc_final: 0.7971 (tm-30) REVERT: A 227 HIS cc_start: 0.8612 (OUTLIER) cc_final: 0.7754 (m90) REVERT: B 134 ARG cc_start: 0.8195 (tpt170) cc_final: 0.7761 (ttt180) REVERT: B 154 TYR cc_start: 0.8312 (t80) cc_final: 0.8013 (t80) REVERT: B 155 ASP cc_start: 0.7982 (p0) cc_final: 0.7403 (p0) REVERT: B 194 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8471 (mt-10) REVERT: B 198 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8413 (mtmt) REVERT: B 218 GLN cc_start: 0.9143 (mm110) cc_final: 0.8919 (mm110) REVERT: B 226 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8010 (tm-30) REVERT: B 227 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.7809 (m90) outliers start: 20 outliers final: 14 residues processed: 99 average time/residue: 0.1593 time to fit residues: 18.7910 Evaluate side-chains 94 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 9 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** 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 = 0.3355 r_free = 0.3355 target = 0.097629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.072944 restraints weight = 6386.209| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.85 r_work: 0.2757 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3296 Z= 0.231 Angle : 0.516 4.997 4488 Z= 0.277 Chirality : 0.041 0.135 504 Planarity : 0.003 0.022 530 Dihedral : 15.749 135.472 480 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 5.20 % Allowed : 24.86 % Favored : 69.94 % 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: 1.74 (0.42), residues: 374 helix: 3.04 (0.37), residues: 180 sheet: 0.27 (0.53), residues: 84 loop : -1.46 (0.47), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.010 0.002 HIS A 227 PHE 0.024 0.002 PHE B 114 TYR 0.010 0.001 TYR B 109 ARG 0.001 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.02818 ( 204) hydrogen bonds : angle 4.24913 ( 594) covalent geometry : bond 0.00519 ( 3296) covalent geometry : angle 0.51596 ( 4488) *********************** 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 96 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.386 Fit side-chains REVERT: A 61 LYS cc_start: 0.9536 (mttm) cc_final: 0.9334 (tttm) REVERT: A 134 ARG cc_start: 0.8184 (tpt170) cc_final: 0.7750 (ttt180) REVERT: A 155 ASP cc_start: 0.8046 (p0) cc_final: 0.7437 (p0) REVERT: A 194 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8443 (tm-30) REVERT: A 198 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8327 (mtmt) REVERT: B 134 ARG cc_start: 0.8191 (tpt170) cc_final: 0.7761 (ttt180) REVERT: B 155 ASP cc_start: 0.8041 (p0) cc_final: 0.7436 (p0) REVERT: B 194 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8457 (tm-30) REVERT: B 198 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8316 (mtmt) REVERT: B 218 GLN cc_start: 0.9205 (mm110) cc_final: 0.8985 (mm110) outliers start: 18 outliers final: 14 residues processed: 94 average time/residue: 0.1652 time to fit residues: 18.4525 Evaluate side-chains 92 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 237 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.100181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.075792 restraints weight = 6331.367| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.83 r_work: 0.2797 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.5068 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= 0.147 Angle : 0.494 5.997 4488 Z= 0.270 Chirality : 0.040 0.136 504 Planarity : 0.003 0.021 530 Dihedral : 15.555 137.569 480 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.62 % Allowed : 24.86 % 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: 1.74 (0.42), residues: 374 helix: 3.01 (0.36), residues: 180 sheet: 0.37 (0.53), residues: 84 loop : -1.50 (0.46), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 128 HIS 0.005 0.001 HIS A 227 PHE 0.023 0.002 PHE B 114 TYR 0.013 0.001 TYR A 154 ARG 0.001 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.02566 ( 204) hydrogen bonds : angle 4.11149 ( 594) covalent geometry : bond 0.00336 ( 3296) covalent geometry : angle 0.49418 ( 4488) *********************** 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 97 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.332 Fit side-chains REVERT: A 61 LYS cc_start: 0.9535 (mttm) cc_final: 0.9298 (tttm) REVERT: A 134 ARG cc_start: 0.8176 (tpt170) cc_final: 0.7725 (ttt180) REVERT: A 154 TYR cc_start: 0.8249 (t80) cc_final: 0.7902 (t80) REVERT: A 155 ASP cc_start: 0.8047 (p0) cc_final: 0.7429 (p0) REVERT: A 194 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8536 (mt-10) REVERT: A 198 LYS cc_start: 0.8617 (mtmt) cc_final: 0.7914 (mmtm) REVERT: A 226 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 227 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.7958 (m90) REVERT: B 134 ARG cc_start: 0.8187 (tpt170) cc_final: 0.7722 (ttt180) REVERT: B 154 TYR cc_start: 0.8268 (t80) cc_final: 0.7919 (t80) REVERT: B 155 ASP cc_start: 0.8051 (p0) cc_final: 0.7428 (p0) REVERT: B 194 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8534 (mt-10) REVERT: B 198 LYS cc_start: 0.8609 (mtmt) cc_final: 0.7908 (mmtm) REVERT: B 218 GLN cc_start: 0.9103 (mm110) cc_final: 0.8902 (mm110) REVERT: B 226 GLU cc_start: 0.8709 (tm-30) cc_final: 0.7997 (tm-30) REVERT: B 227 HIS cc_start: 0.8687 (OUTLIER) cc_final: 0.7779 (m90) outliers start: 16 outliers final: 12 residues processed: 95 average time/residue: 0.1611 time to fit residues: 18.2679 Evaluate side-chains 94 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 10 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 227 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.100265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.075389 restraints weight = 6313.826| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.81 r_work: 0.2774 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 : 0.004 0.039 3296 Z= 0.170 Angle : 0.503 5.984 4488 Z= 0.274 Chirality : 0.040 0.135 504 Planarity : 0.003 0.021 530 Dihedral : 15.587 141.199 480 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.62 % Allowed : 24.86 % 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: 1.71 (0.42), residues: 374 helix: 3.03 (0.37), residues: 180 sheet: 0.27 (0.53), residues: 84 loop : -1.52 (0.46), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 128 HIS 0.004 0.001 HIS A 227 PHE 0.023 0.002 PHE B 114 TYR 0.011 0.001 TYR A 154 ARG 0.001 0.000 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.02629 ( 204) hydrogen bonds : angle 4.13449 ( 594) covalent geometry : bond 0.00388 ( 3296) covalent geometry : angle 0.50316 ( 4488) ********************** 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 96 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.374 Fit side-chains REVERT: A 61 LYS cc_start: 0.9531 (mttm) cc_final: 0.9286 (tttm) REVERT: A 134 ARG cc_start: 0.8216 (tpt170) cc_final: 0.7762 (ttt180) REVERT: A 154 TYR cc_start: 0.8215 (t80) cc_final: 0.7859 (t80) REVERT: A 155 ASP cc_start: 0.8029 (p0) cc_final: 0.7393 (p0) REVERT: A 194 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8552 (mt-10) REVERT: A 198 LYS cc_start: 0.8623 (mtmt) cc_final: 0.7924 (mmtm) REVERT: A 226 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 227 HIS cc_start: 0.8714 (OUTLIER) cc_final: 0.7810 (m90) REVERT: B 134 ARG cc_start: 0.8223 (tpt170) cc_final: 0.7753 (ttt180) REVERT: B 154 TYR cc_start: 0.8230 (t80) cc_final: 0.7883 (t80) REVERT: B 155 ASP cc_start: 0.8043 (p0) cc_final: 0.7400 (p0) REVERT: B 194 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8561 (mt-10) REVERT: B 198 LYS cc_start: 0.8616 (mtmt) cc_final: 0.7954 (mmtm) REVERT: B 226 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8033 (tm-30) REVERT: B 227 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.7788 (m90) outliers start: 16 outliers final: 14 residues processed: 94 average time/residue: 0.1689 time to fit residues: 18.8634 Evaluate side-chains 96 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 75 LYS 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 75 LYS 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 27 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 227 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.075273 restraints weight = 6395.062| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.79 r_work: 0.2781 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3296 Z= 0.151 Angle : 0.493 5.808 4488 Z= 0.270 Chirality : 0.040 0.136 504 Planarity : 0.003 0.021 530 Dihedral : 15.567 144.171 480 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.62 % Allowed : 24.86 % 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: 1.70 (0.42), residues: 374 helix: 3.02 (0.37), residues: 180 sheet: 0.24 (0.53), residues: 84 loop : -1.52 (0.46), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 128 HIS 0.004 0.001 HIS A 227 PHE 0.022 0.002 PHE B 114 TYR 0.010 0.001 TYR A 154 ARG 0.001 0.000 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.02586 ( 204) hydrogen bonds : angle 4.10521 ( 594) covalent geometry : bond 0.00347 ( 3296) covalent geometry : angle 0.49302 ( 4488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1921.43 seconds wall clock time: 34 minutes 12.28 seconds (2052.28 seconds total)