Starting phenix.real_space_refine on Wed Mar 5 20:22:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eqt_28545/03_2025/8eqt_28545_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eqt_28545/03_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_28545/03_2025/8eqt_28545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eqt_28545/03_2025/8eqt_28545.map" model { file = "/net/cci-nas-00/data/ceres_data/8eqt_28545/03_2025/8eqt_28545_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eqt_28545/03_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-5624/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: 2.96, per 1000 atoms: 0.92 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: 0.87 Conformation dependent library (CDL) restraints added in 374.6 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: 0.87 Time building geometry restraints manager: 1.03 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: 0.02 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: 1.390 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.390 Find NCS groups from input model: 0.150 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: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.050 ------------------------------------------------------------------------------- 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 : 0.341 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: 0.1594 time to fit residues: 33.8110 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 : 0.393 ------------------------------------------------------------------------------- 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: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.102309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.077701 restraints weight = 6225.813| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.00 r_work: 0.2822 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3460 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= 0.201 Angle : 0.501 4.354 4488 Z= 0.261 Chirality : 0.040 0.134 504 Planarity : 0.003 0.022 530 Dihedral : 17.479 146.291 480 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: 1.75 (0.41), residues: 374 helix: 2.73 (0.37), residues: 168 sheet: 0.77 (0.57), residues: 86 loop : -0.88 (0.46), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 193 HIS 0.004 0.001 HIS A 78 PHE 0.024 0.002 PHE A 230 TYR 0.007 0.001 TYR B 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 : 0.382 Fit side-chains REVERT: A 102 GLU cc_start: 0.8503 (mp0) cc_final: 0.8091 (mp0) REVERT: A 134 ARG cc_start: 0.8024 (tpt170) cc_final: 0.7543 (ttt180) REVERT: A 154 TYR cc_start: 0.8417 (t80) cc_final: 0.7690 (t80) REVERT: A 194 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8496 (mt-10) REVERT: A 198 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8166 (mtmt) REVERT: A 211 TYR cc_start: 0.8091 (m-80) cc_final: 0.7831 (m-80) REVERT: A 233 TYR cc_start: 0.9607 (m-80) cc_final: 0.9029 (m-80) REVERT: B 102 GLU cc_start: 0.8519 (mp0) cc_final: 0.8102 (mp0) REVERT: B 134 ARG cc_start: 0.8033 (tpt170) cc_final: 0.7563 (ttt180) REVERT: B 154 TYR cc_start: 0.8420 (t80) cc_final: 0.7686 (t80) REVERT: B 194 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8466 (mt-10) REVERT: B 198 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8159 (mtmt) REVERT: B 211 TYR cc_start: 0.8100 (m-80) cc_final: 0.7843 (m-80) REVERT: B 233 TYR cc_start: 0.9607 (m-80) cc_final: 0.9011 (m-80) outliers start: 14 outliers final: 12 residues processed: 124 average time/residue: 0.1656 time to fit residues: 24.2311 Evaluate side-chains 104 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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: 0.7980 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3385 r_free = 0.3385 target = 0.099774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.075709 restraints weight = 6271.783| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.92 r_work: 0.2805 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4044 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 : 0.452 4.420 4488 Z= 0.242 Chirality : 0.040 0.131 504 Planarity : 0.003 0.021 530 Dihedral : 16.714 146.043 480 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.62 % Allowed : 19.36 % Favored : 76.01 % 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: 1.77 (0.41), residues: 374 helix: 2.81 (0.37), residues: 168 sheet: 0.78 (0.58), residues: 86 loop : -0.99 (0.45), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.004 0.001 HIS A 227 PHE 0.015 0.002 PHE B 43 TYR 0.005 0.001 TYR B 109 ARG 0.000 0.000 ARG A 134 *********************** 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: 16 poor density : 114 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 PHE cc_start: 0.9292 (m-80) cc_final: 0.9053 (m-80) REVERT: A 134 ARG cc_start: 0.8098 (tpt170) cc_final: 0.7608 (ttt180) REVERT: A 136 LYS cc_start: 0.8705 (pttt) cc_final: 0.8485 (pttt) REVERT: A 155 ASP cc_start: 0.7899 (p0) cc_final: 0.7446 (p0) REVERT: A 194 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8487 (mt-10) REVERT: A 211 TYR cc_start: 0.8070 (m-80) cc_final: 0.7829 (m-80) REVERT: A 232 ILE cc_start: 0.9374 (mm) cc_final: 0.9050 (mm) REVERT: B 105 PHE cc_start: 0.9292 (m-80) cc_final: 0.9052 (m-80) REVERT: B 134 ARG cc_start: 0.8123 (tpt170) cc_final: 0.7607 (ttt180) REVERT: B 136 LYS cc_start: 0.8701 (pttt) cc_final: 0.8483 (pttt) REVERT: B 155 ASP cc_start: 0.7907 (p0) cc_final: 0.7467 (p0) REVERT: B 194 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8483 (mt-10) REVERT: B 211 TYR cc_start: 0.8071 (m-80) cc_final: 0.7831 (m-80) REVERT: B 232 ILE cc_start: 0.9365 (mm) cc_final: 0.9029 (mm) outliers start: 16 outliers final: 14 residues processed: 126 average time/residue: 0.1566 time to fit residues: 23.6253 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 : 0.396 ------------------------------------------------------------------------------- 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: 0.4980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.102687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.078627 restraints weight = 6148.230| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.76 r_work: 0.2818 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3296 Z= 0.210 Angle : 0.467 5.244 4488 Z= 0.251 Chirality : 0.039 0.136 504 Planarity : 0.003 0.020 530 Dihedral : 16.347 144.740 480 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.62 % Allowed : 21.97 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.41), residues: 374 helix: 2.95 (0.36), residues: 168 sheet: 0.62 (0.57), residues: 86 loop : -1.16 (0.44), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.003 0.002 HIS B 227 PHE 0.017 0.002 PHE B 114 TYR 0.005 0.001 TYR A 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 106 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.379 Fit side-chains REVERT: A 102 GLU cc_start: 0.8392 (mp0) cc_final: 0.7997 (mp0) REVERT: A 134 ARG cc_start: 0.8141 (tpt170) cc_final: 0.7557 (ttt180) REVERT: A 154 TYR cc_start: 0.8393 (t80) cc_final: 0.7976 (t80) REVERT: A 155 ASP cc_start: 0.7880 (p0) cc_final: 0.7353 (p0) REVERT: A 211 TYR cc_start: 0.8196 (m-80) cc_final: 0.7936 (m-80) REVERT: A 226 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8095 (tm-30) REVERT: A 227 HIS cc_start: 0.8608 (OUTLIER) cc_final: 0.7786 (m90) REVERT: B 102 GLU cc_start: 0.8382 (mp0) cc_final: 0.7987 (mp0) REVERT: B 134 ARG cc_start: 0.8145 (tpt170) cc_final: 0.7568 (ttt180) REVERT: B 154 TYR cc_start: 0.8408 (t80) cc_final: 0.7995 (t80) REVERT: B 155 ASP cc_start: 0.7882 (p0) cc_final: 0.7355 (p0) REVERT: B 211 TYR cc_start: 0.8200 (m-80) cc_final: 0.7940 (m-80) REVERT: B 226 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8120 (tm-30) REVERT: B 227 HIS cc_start: 0.8614 (OUTLIER) cc_final: 0.7801 (m90) outliers start: 16 outliers final: 14 residues processed: 100 average time/residue: 0.1737 time to fit residues: 20.6637 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 : 0.345 ------------------------------------------------------------------------------- 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 97 VAL 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 97 VAL 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 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.102409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.077914 restraints weight = 6087.752| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.80 r_work: 0.2829 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3296 Z= 0.187 Angle : 0.433 4.577 4488 Z= 0.236 Chirality : 0.039 0.134 504 Planarity : 0.003 0.020 530 Dihedral : 15.995 140.200 480 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.85 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: 1.85 (0.41), residues: 374 helix: 2.72 (0.35), residues: 192 sheet: 0.68 (0.54), residues: 84 loop : -1.44 (0.48), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 193 HIS 0.010 0.002 HIS B 227 PHE 0.018 0.002 PHE A 114 TYR 0.006 0.001 TYR A 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 104 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8197 (tpt170) cc_final: 0.7718 (ttt180) REVERT: A 155 ASP cc_start: 0.8044 (p0) cc_final: 0.7494 (p0) REVERT: A 194 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8372 (tm-30) REVERT: A 211 TYR cc_start: 0.8214 (m-80) cc_final: 0.7982 (m-80) REVERT: B 134 ARG cc_start: 0.8219 (tpt170) cc_final: 0.7720 (ttt180) REVERT: B 155 ASP cc_start: 0.8053 (p0) cc_final: 0.7496 (p0) REVERT: B 194 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8364 (tm-30) REVERT: B 211 TYR cc_start: 0.8223 (m-80) cc_final: 0.7991 (m-80) REVERT: B 218 GLN cc_start: 0.9177 (mm110) cc_final: 0.8929 (mm110) outliers start: 18 outliers final: 16 residues processed: 100 average time/residue: 0.1732 time to fit residues: 20.5663 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 : 0.387 ------------------------------------------------------------------------------- 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 192 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 0.0770 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.102753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.077627 restraints weight = 6305.098| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.93 r_work: 0.2833 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4824 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= 0.154 Angle : 0.439 4.544 4488 Z= 0.240 Chirality : 0.039 0.135 504 Planarity : 0.003 0.020 530 Dihedral : 15.724 134.861 480 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 4.05 % Allowed : 26.01 % 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: 1.94 (0.42), residues: 374 helix: 2.90 (0.36), residues: 192 sheet: 0.69 (0.53), residues: 84 loop : -1.63 (0.49), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 193 HIS 0.007 0.002 HIS B 227 PHE 0.024 0.002 PHE A 114 TYR 0.004 0.001 TYR B 154 ARG 0.000 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 106 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8220 (tpt170) cc_final: 0.7723 (ttt180) REVERT: A 155 ASP cc_start: 0.8060 (p0) cc_final: 0.7645 (p0) REVERT: A 194 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8353 (tm-30) REVERT: A 198 LYS cc_start: 0.8585 (mtmt) cc_final: 0.7983 (mmtm) REVERT: A 218 GLN cc_start: 0.9171 (mm110) cc_final: 0.8913 (mm110) REVERT: B 134 ARG cc_start: 0.8232 (tpt170) cc_final: 0.7723 (ttt180) REVERT: B 155 ASP cc_start: 0.8070 (p0) cc_final: 0.7654 (p0) REVERT: B 194 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8346 (tm-30) REVERT: B 198 LYS cc_start: 0.8583 (mtmt) cc_final: 0.7981 (mmtm) REVERT: B 218 GLN cc_start: 0.9094 (mm110) cc_final: 0.8858 (mm110) outliers start: 14 outliers final: 14 residues processed: 104 average time/residue: 0.1602 time to fit residues: 19.8384 Evaluate side-chains 96 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 192 LYS 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 192 LYS 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: 0.6980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS A 227 HIS B 204 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 = 0.3406 r_free = 0.3406 target = 0.100856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.075992 restraints weight = 6280.921| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.88 r_work: 0.2817 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3296 Z= 0.206 Angle : 0.449 4.516 4488 Z= 0.245 Chirality : 0.039 0.134 504 Planarity : 0.003 0.020 530 Dihedral : 15.711 146.515 480 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.62 % Allowed : 26.01 % Favored : 69.36 % 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: 1.97 (0.42), residues: 374 helix: 3.21 (0.36), residues: 180 sheet: 0.65 (0.52), residues: 84 loop : -1.58 (0.46), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.008 0.002 HIS B 227 PHE 0.026 0.002 PHE B 114 TYR 0.007 0.001 TYR B 154 ARG 0.001 0.000 ARG B 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 99 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.352 Fit side-chains REVERT: A 61 LYS cc_start: 0.9436 (ttmm) cc_final: 0.9037 (mttm) REVERT: A 134 ARG cc_start: 0.8213 (tpt170) cc_final: 0.7747 (ttt180) REVERT: A 154 TYR cc_start: 0.8623 (t80) cc_final: 0.8271 (t80) REVERT: A 155 ASP cc_start: 0.8181 (p0) cc_final: 0.7682 (p0) REVERT: A 194 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8607 (mp0) REVERT: A 218 GLN cc_start: 0.9146 (mm110) cc_final: 0.8888 (mm110) REVERT: A 227 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.7824 (m90) REVERT: B 61 LYS cc_start: 0.9433 (ttmm) cc_final: 0.9017 (mttm) REVERT: B 134 ARG cc_start: 0.8221 (tpt170) cc_final: 0.7740 (ttt180) REVERT: B 154 TYR cc_start: 0.8642 (t80) cc_final: 0.8294 (t80) REVERT: B 155 ASP cc_start: 0.8201 (p0) cc_final: 0.7705 (p0) REVERT: B 194 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8600 (mp0) REVERT: B 218 GLN cc_start: 0.9029 (mm110) cc_final: 0.8804 (mm110) REVERT: B 227 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.7773 (m90) outliers start: 16 outliers final: 12 residues processed: 97 average time/residue: 0.1603 time to fit residues: 18.9327 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 : 0.349 ------------------------------------------------------------------------------- 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=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: 0.0980 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: 0.5980 chunk 15 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.102854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.078229 restraints weight = 6196.813| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.85 r_work: 0.2846 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 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 : 0.003 0.024 3296 Z= 0.163 Angle : 0.452 5.618 4488 Z= 0.249 Chirality : 0.039 0.139 504 Planarity : 0.002 0.020 530 Dihedral : 15.555 151.493 480 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.20 % Allowed : 25.43 % Favored : 69.36 % 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: 1.96 (0.42), residues: 374 helix: 3.20 (0.36), residues: 180 sheet: 0.65 (0.53), residues: 84 loop : -1.58 (0.46), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.007 0.001 HIS B 227 PHE 0.026 0.002 PHE A 114 TYR 0.005 0.001 TYR A 154 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 99 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.358 Fit side-chains REVERT: A 61 LYS cc_start: 0.9427 (ttmm) cc_final: 0.9208 (ttmm) REVERT: A 134 ARG cc_start: 0.8180 (tpt170) cc_final: 0.7738 (ttt180) REVERT: A 154 TYR cc_start: 0.8585 (t80) cc_final: 0.8151 (t80) REVERT: A 155 ASP cc_start: 0.8148 (p0) cc_final: 0.7670 (p0) REVERT: A 194 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8588 (mp0) REVERT: A 218 GLN cc_start: 0.9070 (mm110) cc_final: 0.8852 (mm110) REVERT: A 226 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8119 (tp30) REVERT: A 227 HIS cc_start: 0.8659 (OUTLIER) cc_final: 0.7840 (m90) REVERT: B 61 LYS cc_start: 0.9385 (ttmm) cc_final: 0.9182 (ttmm) REVERT: B 134 ARG cc_start: 0.8203 (tpt170) cc_final: 0.7735 (ttt180) REVERT: B 154 TYR cc_start: 0.8602 (t80) cc_final: 0.8169 (t80) REVERT: B 155 ASP cc_start: 0.8168 (p0) cc_final: 0.7681 (p0) REVERT: B 194 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8574 (mp0) REVERT: B 198 LYS cc_start: 0.8615 (mtmt) cc_final: 0.7990 (mmtm) REVERT: B 226 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8091 (tp30) REVERT: B 227 HIS cc_start: 0.8635 (OUTLIER) cc_final: 0.7814 (m90) outliers start: 18 outliers final: 12 residues processed: 97 average time/residue: 0.1634 time to fit residues: 18.8468 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 : 0.350 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS A 227 HIS B 227 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.101384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.076781 restraints weight = 6283.433| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 3.85 r_work: 0.2827 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.5055 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= 0.212 Angle : 0.472 6.129 4488 Z= 0.257 Chirality : 0.039 0.137 504 Planarity : 0.003 0.020 530 Dihedral : 15.522 155.344 480 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.62 % Allowed : 26.01 % Favored : 69.36 % 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 (0.42), residues: 374 helix: 3.25 (0.37), residues: 180 sheet: 0.63 (0.53), residues: 84 loop : -1.60 (0.45), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 128 HIS 0.009 0.002 HIS B 227 PHE 0.024 0.002 PHE A 114 TYR 0.005 0.001 TYR A 160 ARG 0.001 0.000 ARG B 126 *********************** 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 96 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.383 Fit side-chains REVERT: A 134 ARG cc_start: 0.8177 (tpt170) cc_final: 0.7717 (ttt180) REVERT: A 154 TYR cc_start: 0.8557 (t80) cc_final: 0.8089 (t80) REVERT: A 155 ASP cc_start: 0.8080 (p0) cc_final: 0.7603 (p0) REVERT: A 194 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8575 (mp0) REVERT: A 198 LYS cc_start: 0.8742 (mttt) cc_final: 0.8150 (mmtt) REVERT: A 218 GLN cc_start: 0.9205 (mm110) cc_final: 0.9002 (mm110) REVERT: A 227 HIS cc_start: 0.8676 (OUTLIER) cc_final: 0.7705 (m90) REVERT: B 61 LYS cc_start: 0.9368 (ttmm) cc_final: 0.9145 (ttmm) REVERT: B 134 ARG cc_start: 0.8211 (tpt170) cc_final: 0.7727 (ttt180) REVERT: B 154 TYR cc_start: 0.8554 (t80) cc_final: 0.8080 (t80) REVERT: B 155 ASP cc_start: 0.8165 (p0) cc_final: 0.7678 (p0) REVERT: B 194 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8562 (mp0) REVERT: B 198 LYS cc_start: 0.8646 (mtmt) cc_final: 0.8010 (mmtm) REVERT: B 226 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8133 (tp30) REVERT: B 227 HIS cc_start: 0.8659 (OUTLIER) cc_final: 0.7748 (m90) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 0.1672 time to fit residues: 19.1023 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 : 0.348 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 0.0470 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.102010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.077258 restraints weight = 6250.382| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.85 r_work: 0.2833 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.5088 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= 0.195 Angle : 0.489 7.652 4488 Z= 0.267 Chirality : 0.040 0.137 504 Planarity : 0.002 0.020 530 Dihedral : 15.521 159.041 480 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.62 % Allowed : 25.72 % Favored : 69.65 % 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: 1.99 (0.42), residues: 374 helix: 3.23 (0.37), residues: 180 sheet: 0.73 (0.54), residues: 84 loop : -1.64 (0.45), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 128 HIS 0.003 0.001 HIS A 150 PHE 0.024 0.002 PHE A 114 TYR 0.005 0.001 TYR B 206 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 96 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.384 Fit side-chains REVERT: A 102 GLU cc_start: 0.8478 (mp0) cc_final: 0.8005 (mp0) REVERT: A 134 ARG cc_start: 0.8172 (tpt170) cc_final: 0.7721 (ttt180) REVERT: A 154 TYR cc_start: 0.8510 (t80) cc_final: 0.8069 (t80) REVERT: A 155 ASP cc_start: 0.8071 (p0) cc_final: 0.7596 (p0) REVERT: A 194 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8581 (mp0) REVERT: A 198 LYS cc_start: 0.8700 (mttt) cc_final: 0.8130 (mmtt) REVERT: A 226 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8114 (tp30) REVERT: A 227 HIS cc_start: 0.8708 (OUTLIER) cc_final: 0.7734 (m90) REVERT: B 61 LYS cc_start: 0.9350 (ttmm) cc_final: 0.9136 (ttmm) REVERT: B 134 ARG cc_start: 0.8197 (tpt170) cc_final: 0.7713 (ttt180) REVERT: B 154 TYR cc_start: 0.8506 (t80) cc_final: 0.8108 (t80) REVERT: B 155 ASP cc_start: 0.8155 (p0) cc_final: 0.7667 (p0) REVERT: B 194 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8565 (mp0) REVERT: B 198 LYS cc_start: 0.8643 (mtmt) cc_final: 0.7996 (mmtm) REVERT: B 226 GLU cc_start: 0.8549 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 227 HIS cc_start: 0.8683 (OUTLIER) cc_final: 0.7658 (m90) outliers start: 16 outliers final: 12 residues processed: 95 average time/residue: 0.1775 time to fit residues: 20.0040 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 : 0.391 ------------------------------------------------------------------------------- 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 86 LEU 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: 1.9990 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** B 218 GLN ** 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 = 0.3421 r_free = 0.3421 target = 0.101651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.076659 restraints weight = 6370.599| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.91 r_work: 0.2820 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3296 Z= 0.203 Angle : 0.477 6.926 4488 Z= 0.261 Chirality : 0.039 0.137 504 Planarity : 0.003 0.022 530 Dihedral : 15.560 162.661 480 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.20 % Allowed : 26.01 % Favored : 68.79 % 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: 1.99 (0.42), residues: 374 helix: 3.21 (0.37), residues: 180 sheet: 0.73 (0.53), residues: 84 loop : -1.60 (0.45), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.007 0.001 HIS B 227 PHE 0.024 0.002 PHE A 114 TYR 0.005 0.001 TYR B 206 ARG 0.001 0.000 ARG A 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1905.91 seconds wall clock time: 33 minutes 45.31 seconds (2025.31 seconds total)