Starting phenix.real_space_refine on Fri Dec 27 21:02:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ifu_35423/12_2024/8ifu_35423_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ifu_35423/12_2024/8ifu_35423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ifu_35423/12_2024/8ifu_35423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ifu_35423/12_2024/8ifu_35423.map" model { file = "/net/cci-nas-00/data/ceres_data/8ifu_35423/12_2024/8ifu_35423_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ifu_35423/12_2024/8ifu_35423_neut.cif" } resolution = 2.37 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= 0.029 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 42 5.16 5 Na 48 4.78 5 C 4548 2.51 5 N 978 2.21 5 O 1110 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6732 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2095 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 14, 'TRANS': 244} Chain: "B" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2095 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 14, 'TRANS': 244} Chain: "C" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2095 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 14, 'TRANS': 244} Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 138 Unusual residues: {' NA': 16, 'L9Q': 2, 'RET': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 138 Unusual residues: {' NA': 16, 'L9Q': 2, 'RET': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 138 Unusual residues: {' NA': 16, 'L9Q': 2, 'RET': 1} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Time building chain proxies: 6.57, per 1000 atoms: 0.98 Number of scatterers: 6732 At special positions: 0 Unit cell: (74.67, 74.67, 80.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 6 15.00 Na 48 11.00 O 1110 8.00 N 978 7.00 C 4548 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 969.5 milliseconds 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1416 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 72.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 21 through 50 removed outlier: 4.076A pdb=" N GLY A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 Processing helix chain 'A' and resid 68 through 90 Processing helix chain 'A' and resid 103 through 121 removed outlier: 3.730A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 150 through 178 Proline residue: A 164 - end of helix removed outlier: 3.859A pdb=" N GLN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 196 removed outlier: 3.620A pdb=" N ILE A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 194 " --> pdb=" O TRP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 removed outlier: 3.921A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 50 removed outlier: 4.076A pdb=" N GLY B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 67 Processing helix chain 'B' and resid 68 through 90 Processing helix chain 'B' and resid 103 through 121 removed outlier: 3.730A pdb=" N PHE B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 150 through 178 Proline residue: B 164 - end of helix removed outlier: 3.858A pdb=" N GLN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 removed outlier: 3.620A pdb=" N ILE B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 194 " --> pdb=" O TRP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 removed outlier: 3.921A pdb=" N ILE B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 50 removed outlier: 4.077A pdb=" N GLY C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 67 Processing helix chain 'C' and resid 68 through 90 Processing helix chain 'C' and resid 103 through 121 removed outlier: 3.730A pdb=" N PHE C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 150 through 178 Proline residue: C 164 - end of helix removed outlier: 3.859A pdb=" N GLN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 196 removed outlier: 3.619A pdb=" N ILE C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 194 " --> pdb=" O TRP C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 removed outlier: 3.921A pdb=" N ILE C 204 " --> pdb=" O PRO C 200 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 405 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1026 1.32 - 1.44: 2241 1.44 - 1.56: 3561 1.56 - 1.69: 18 1.69 - 1.81: 54 Bond restraints: 6900 Sorted by residual: bond pdb=" C39 L9Q B 301 " pdb=" C40 L9Q B 301 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" C39 L9Q C 302 " pdb=" C40 L9Q C 302 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C39 L9Q A 319 " pdb=" C40 L9Q A 319 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C39 L9Q B 319 " pdb=" C40 L9Q B 319 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" C39 L9Q C 301 " pdb=" C40 L9Q C 301 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.89e+01 ... (remaining 6895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.76: 9171 5.76 - 11.51: 126 11.51 - 17.27: 21 17.27 - 23.03: 6 23.03 - 28.78: 6 Bond angle restraints: 9330 Sorted by residual: angle pdb=" C17 RET C 303 " pdb=" C1 RET C 303 " pdb=" C6 RET C 303 " ideal model delta sigma weight residual 110.87 82.09 28.78 3.00e+00 1.11e-01 9.20e+01 angle pdb=" C17 RET B 302 " pdb=" C1 RET B 302 " pdb=" C6 RET B 302 " ideal model delta sigma weight residual 110.87 82.09 28.78 3.00e+00 1.11e-01 9.20e+01 angle pdb=" C17 RET A 301 " pdb=" C1 RET A 301 " pdb=" C6 RET A 301 " ideal model delta sigma weight residual 110.87 82.10 28.77 3.00e+00 1.11e-01 9.20e+01 angle pdb=" C16 RET B 302 " pdb=" C1 RET B 302 " pdb=" C17 RET B 302 " ideal model delta sigma weight residual 109.83 84.95 24.88 3.00e+00 1.11e-01 6.88e+01 angle pdb=" C16 RET A 301 " pdb=" C1 RET A 301 " pdb=" C17 RET A 301 " ideal model delta sigma weight residual 109.83 84.95 24.88 3.00e+00 1.11e-01 6.88e+01 ... (remaining 9325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 3527 35.19 - 70.38: 301 70.38 - 105.57: 27 105.57 - 140.75: 9 140.75 - 175.94: 18 Dihedral angle restraints: 3882 sinusoidal: 1653 harmonic: 2229 Sorted by residual: dihedral pdb=" C GLU B 248 " pdb=" N GLU B 248 " pdb=" CA GLU B 248 " pdb=" CB GLU B 248 " ideal model delta harmonic sigma weight residual -122.60 -134.82 12.22 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" C GLU C 248 " pdb=" N GLU C 248 " pdb=" CA GLU C 248 " pdb=" CB GLU C 248 " ideal model delta harmonic sigma weight residual -122.60 -134.80 12.20 0 2.50e+00 1.60e-01 2.38e+01 dihedral pdb=" C GLU A 248 " pdb=" N GLU A 248 " pdb=" CA GLU A 248 " pdb=" CB GLU A 248 " ideal model delta harmonic sigma weight residual -122.60 -134.80 12.20 0 2.50e+00 1.60e-01 2.38e+01 ... (remaining 3879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 620 0.116 - 0.232: 255 0.232 - 0.348: 37 0.348 - 0.463: 15 0.463 - 0.579: 9 Chirality restraints: 936 Sorted by residual: chirality pdb=" CA GLU A 248 " pdb=" N GLU A 248 " pdb=" C GLU A 248 " pdb=" CB GLU A 248 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" CA GLU C 248 " pdb=" N GLU C 248 " pdb=" C GLU C 248 " pdb=" CB GLU C 248 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.38e+00 chirality pdb=" CA GLU B 248 " pdb=" N GLU B 248 " pdb=" C GLU B 248 " pdb=" CB GLU B 248 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.37e+00 ... (remaining 933 not shown) Planarity restraints: 1131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 L9Q C 301 " 0.336 2.00e-02 2.50e+03 3.25e-01 1.06e+03 pdb=" C39 L9Q C 301 " -0.364 2.00e-02 2.50e+03 pdb=" C40 L9Q C 301 " -0.284 2.00e-02 2.50e+03 pdb=" C41 L9Q C 301 " 0.312 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q A 318 " 0.336 2.00e-02 2.50e+03 3.25e-01 1.06e+03 pdb=" C39 L9Q A 318 " -0.366 2.00e-02 2.50e+03 pdb=" C40 L9Q A 318 " -0.282 2.00e-02 2.50e+03 pdb=" C41 L9Q A 318 " 0.312 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 L9Q B 319 " -0.336 2.00e-02 2.50e+03 3.25e-01 1.06e+03 pdb=" C39 L9Q B 319 " 0.365 2.00e-02 2.50e+03 pdb=" C40 L9Q B 319 " 0.283 2.00e-02 2.50e+03 pdb=" C41 L9Q B 319 " -0.312 2.00e-02 2.50e+03 ... (remaining 1128 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.11: 30 2.11 - 2.81: 2166 2.81 - 3.51: 8981 3.51 - 4.20: 18754 4.20 - 4.90: 31681 Nonbonded interactions: 61612 Sorted by model distance: nonbonded pdb=" C40 L9Q A 319 " pdb=" C40 L9Q B 301 " model vdw 1.417 2.912 nonbonded pdb=" C40 L9Q B 301 " pdb=" C40 L9Q C 302 " model vdw 1.417 2.912 nonbonded pdb=" C45 L9Q B 301 " pdb=" C27 L9Q B 319 " model vdw 1.489 3.840 nonbonded pdb=" C27 L9Q A 318 " pdb=" C45 L9Q A 319 " model vdw 1.490 3.840 nonbonded pdb=" C27 L9Q C 301 " pdb=" C45 L9Q C 302 " model vdw 1.490 3.840 ... (remaining 61607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 260 or resid 304 through 317)) selection = (chain 'B' and (resid 2 through 260 or resid 304 through 317)) selection = (chain 'C' and (resid 2 through 260 or resid 304 through 317)) } 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: 6.740 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.270 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.017 0.190 6900 Z= 1.069 Angle : 1.972 28.782 9330 Z= 1.024 Chirality : 0.136 0.579 936 Planarity : 0.021 0.325 1131 Dihedral : 27.728 175.942 2466 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.72 % Favored : 96.89 % Rotamer: Outliers : 16.44 % Allowed : 10.05 % Favored : 73.52 % Cbeta Deviations : 1.69 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.25), residues: 771 helix: -1.99 (0.17), residues: 525 sheet: None (None), residues: 0 loop : -1.22 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP B 199 HIS 0.008 0.002 HIS A 250 PHE 0.034 0.003 PHE B 165 TYR 0.024 0.003 TYR A 177 ARG 0.003 0.001 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 122 time to evaluate : 0.849 Fit side-chains REVERT: A 254 LEU cc_start: 0.8419 (mt) cc_final: 0.8194 (mp) REVERT: B 254 LEU cc_start: 0.8361 (mt) cc_final: 0.8127 (mp) REVERT: C 98 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: C 254 LEU cc_start: 0.8404 (mt) cc_final: 0.8202 (mp) outliers start: 108 outliers final: 17 residues processed: 194 average time/residue: 0.9789 time to fit residues: 203.0040 Evaluate side-chains 118 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 234 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS B 125 HIS B 219 GLN C 125 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6900 Z= 0.229 Angle : 0.720 10.218 9330 Z= 0.341 Chirality : 0.043 0.153 936 Planarity : 0.007 0.048 1131 Dihedral : 26.681 143.956 1157 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 6.24 % Allowed : 14.00 % Favored : 79.76 % 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: 0.34 (0.29), residues: 771 helix: 0.62 (0.20), residues: 543 sheet: None (None), residues: 0 loop : -0.51 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 42 HIS 0.003 0.001 HIS A 250 PHE 0.018 0.002 PHE C 167 TYR 0.014 0.002 TYR C 180 ARG 0.004 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.771 Fit side-chains REVERT: A 9 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6646 (pp20) REVERT: A 254 LEU cc_start: 0.8539 (mt) cc_final: 0.8293 (mp) REVERT: B 9 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6594 (pp20) REVERT: C 9 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6643 (pp20) REVERT: C 171 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7834 (ttm110) REVERT: C 252 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7210 (mt-10) outliers start: 41 outliers final: 16 residues processed: 144 average time/residue: 0.9874 time to fit residues: 151.4838 Evaluate side-chains 114 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6900 Z= 0.209 Angle : 0.642 8.549 9330 Z= 0.299 Chirality : 0.041 0.139 936 Planarity : 0.006 0.043 1131 Dihedral : 22.735 131.449 1154 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 5.94 % Allowed : 13.39 % Favored : 80.67 % 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: 1.83 (0.30), residues: 771 helix: 1.88 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -0.17 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 42 HIS 0.003 0.001 HIS C 250 PHE 0.017 0.002 PHE C 167 TYR 0.012 0.002 TYR C 180 ARG 0.003 0.001 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 0.748 Fit side-chains REVERT: A 9 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6840 (pp20) REVERT: B 9 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6738 (pp20) REVERT: C 9 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6790 (pp20) REVERT: C 171 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7870 (ttm110) REVERT: C 252 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7171 (mt-10) outliers start: 39 outliers final: 19 residues processed: 133 average time/residue: 1.0208 time to fit residues: 144.6270 Evaluate side-chains 116 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 PHE Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6900 Z= 0.206 Angle : 0.626 8.000 9330 Z= 0.292 Chirality : 0.041 0.158 936 Planarity : 0.005 0.037 1131 Dihedral : 20.019 142.346 1151 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 5.63 % Allowed : 12.63 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.31), residues: 771 helix: 2.04 (0.22), residues: 543 sheet: None (None), residues: 0 loop : 0.10 (0.45), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 42 HIS 0.003 0.001 HIS B 172 PHE 0.013 0.001 PHE B 167 TYR 0.013 0.002 TYR C 180 ARG 0.002 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.788 Fit side-chains REVERT: A 252 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6941 (mt-10) REVERT: B 9 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6735 (pp20) REVERT: C 9 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6769 (pp20) REVERT: C 252 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7169 (mt-10) outliers start: 37 outliers final: 17 residues processed: 132 average time/residue: 1.0894 time to fit residues: 152.3407 Evaluate side-chains 114 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6900 Z= 0.207 Angle : 0.611 7.454 9330 Z= 0.286 Chirality : 0.041 0.154 936 Planarity : 0.005 0.036 1131 Dihedral : 19.484 146.663 1148 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 4.72 % Allowed : 13.85 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.31), residues: 771 helix: 2.37 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.12 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 42 HIS 0.002 0.001 HIS C 172 PHE 0.013 0.001 PHE B 167 TYR 0.011 0.002 TYR A 180 ARG 0.002 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.782 Fit side-chains REVERT: A 252 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6782 (mt-10) REVERT: B 9 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6737 (pp20) REVERT: B 252 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: C 9 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6755 (pp20) REVERT: C 252 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7141 (mt-10) outliers start: 31 outliers final: 18 residues processed: 127 average time/residue: 1.0376 time to fit residues: 139.9222 Evaluate side-chains 117 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6900 Z= 0.219 Angle : 0.617 7.555 9330 Z= 0.290 Chirality : 0.042 0.157 936 Planarity : 0.005 0.035 1131 Dihedral : 19.245 152.224 1148 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 4.72 % Allowed : 13.85 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.31), residues: 771 helix: 2.35 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.09 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 42 HIS 0.002 0.001 HIS A 225 PHE 0.012 0.001 PHE A 167 TYR 0.012 0.002 TYR B 177 ARG 0.002 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.724 Fit side-chains REVERT: A 252 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6869 (mt-10) REVERT: B 9 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6762 (pp20) REVERT: B 252 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6904 (mt-10) REVERT: C 9 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6786 (pp20) REVERT: C 252 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6880 (mt-10) outliers start: 31 outliers final: 17 residues processed: 124 average time/residue: 1.0500 time to fit residues: 138.3045 Evaluate side-chains 115 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6900 Z= 0.201 Angle : 0.591 7.340 9330 Z= 0.279 Chirality : 0.041 0.141 936 Planarity : 0.005 0.035 1131 Dihedral : 18.776 157.704 1148 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 4.26 % Allowed : 14.31 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.31), residues: 771 helix: 2.43 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.19 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 42 HIS 0.002 0.001 HIS C 225 PHE 0.012 0.001 PHE A 167 TYR 0.010 0.002 TYR B 22 ARG 0.003 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.716 Fit side-chains REVERT: A 183 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7527 (ttmt) REVERT: A 252 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6879 (mt-10) REVERT: C 252 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6851 (mt-10) outliers start: 28 outliers final: 17 residues processed: 122 average time/residue: 1.0819 time to fit residues: 140.1023 Evaluate side-chains 114 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6900 Z= 0.213 Angle : 0.601 6.414 9330 Z= 0.285 Chirality : 0.042 0.173 936 Planarity : 0.005 0.034 1131 Dihedral : 18.333 160.519 1142 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 3.35 % Allowed : 15.53 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.31), residues: 771 helix: 2.36 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.21 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 42 HIS 0.002 0.001 HIS C 225 PHE 0.013 0.001 PHE A 167 TYR 0.011 0.002 TYR B 177 ARG 0.002 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.916 Fit side-chains REVERT: A 183 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7527 (ttmt) REVERT: A 252 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6841 (mt-10) REVERT: C 252 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6849 (mt-10) outliers start: 22 outliers final: 17 residues processed: 118 average time/residue: 1.0630 time to fit residues: 133.3729 Evaluate side-chains 114 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 4.9990 chunk 40 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6900 Z= 0.172 Angle : 0.559 5.886 9330 Z= 0.266 Chirality : 0.040 0.164 936 Planarity : 0.005 0.035 1131 Dihedral : 17.895 163.295 1142 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 3.65 % Allowed : 15.07 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.31), residues: 771 helix: 2.53 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.30 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 42 HIS 0.002 0.001 HIS C 225 PHE 0.012 0.001 PHE A 167 TYR 0.009 0.002 TYR B 22 ARG 0.003 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.793 Fit side-chains REVERT: A 183 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7481 (ttmt) REVERT: A 252 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6912 (mt-10) REVERT: C 252 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6836 (mt-10) outliers start: 24 outliers final: 18 residues processed: 120 average time/residue: 1.0456 time to fit residues: 133.6632 Evaluate side-chains 116 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 6 optimal weight: 0.0010 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS C 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6900 Z= 0.165 Angle : 0.544 5.540 9330 Z= 0.260 Chirality : 0.039 0.167 936 Planarity : 0.005 0.036 1131 Dihedral : 17.640 163.485 1142 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.35 % Allowed : 15.07 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.31), residues: 771 helix: 2.59 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.35 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 42 HIS 0.002 0.000 HIS B 225 PHE 0.012 0.001 PHE A 167 TYR 0.009 0.001 TYR C 103 ARG 0.004 0.000 ARG A 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.768 Fit side-chains REVERT: A 25 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8028 (mp) REVERT: A 183 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7490 (ttmt) REVERT: A 252 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6901 (mt-10) REVERT: C 252 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6820 (mt-10) outliers start: 22 outliers final: 16 residues processed: 124 average time/residue: 0.9724 time to fit residues: 128.5892 Evaluate side-chains 119 residues out of total 657 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 183 LYS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 252 GLU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 252 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3440 r_free = 0.3440 target = 0.126858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111178 restraints weight = 6239.265| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.20 r_work: 0.3130 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6900 Z= 0.171 Angle : 0.544 5.237 9330 Z= 0.261 Chirality : 0.040 0.169 936 Planarity : 0.005 0.035 1131 Dihedral : 17.525 162.390 1142 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.20 % Allowed : 15.22 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.31), residues: 771 helix: 2.59 (0.22), residues: 522 sheet: None (None), residues: 0 loop : 0.39 (0.44), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 42 HIS 0.002 0.000 HIS C 250 PHE 0.011 0.001 PHE A 167 TYR 0.010 0.002 TYR C 103 ARG 0.003 0.001 ARG B 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3129.15 seconds wall clock time: 56 minutes 58.14 seconds (3418.14 seconds total)