Starting phenix.real_space_refine on Mon Sep 23 23:32:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/09_2024/8gyw_34378.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/09_2024/8gyw_34378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/09_2024/8gyw_34378.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/09_2024/8gyw_34378.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/09_2024/8gyw_34378.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gyw_34378/09_2024/8gyw_34378.cif" } resolution = 3.9 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= 0.005 sd= 0.102 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 4 5.49 5 Mg 4 5.21 5 S 48 5.16 5 C 3994 2.51 5 N 984 2.21 5 O 1042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6076 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3005 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'CDC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 4.95, per 1000 atoms: 0.81 Number of scatterers: 6076 At special positions: 0 Unit cell: (97.37, 101.65, 71.69, 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 48 16.00 P 4 15.00 Mg 4 11.99 O 1042 8.00 N 984 7.00 C 3994 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: 1.53 Conformation dependent library (CDL) restraints added in 718.6 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 80.7% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'B' and resid 28 through 37 Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 64 through 79 removed outlier: 3.539A pdb=" N MET B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 107 removed outlier: 3.756A pdb=" N ILE B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 143 removed outlier: 3.904A pdb=" N TYR B 119 " --> pdb=" O PRO B 115 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY B 137 " --> pdb=" O ASP B 133 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 173 removed outlier: 3.583A pdb=" N LEU B 160 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 177 removed outlier: 3.663A pdb=" N THR B 177 " --> pdb=" O GLN B 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 177' Processing helix chain 'B' and resid 178 through 204 Processing helix chain 'B' and resid 212 through 237 Proline residue: B 232 - end of helix Processing helix chain 'B' and resid 247 through 272 removed outlier: 4.189A pdb=" N ALA B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 307 removed outlier: 3.883A pdb=" N LEU B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 315 through 341 Processing helix chain 'B' and resid 348 through 350 No H-bonds generated for 'chain 'B' and resid 348 through 350' Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 368 through 400 Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.539A pdb=" N MET A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 removed outlier: 3.756A pdb=" N ILE A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 143 removed outlier: 3.904A pdb=" N TYR A 119 " --> pdb=" O PRO A 115 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 173 removed outlier: 3.583A pdb=" N LEU A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 removed outlier: 3.663A pdb=" N THR A 177 " --> pdb=" O GLN A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 177' Processing helix chain 'A' and resid 178 through 204 Processing helix chain 'A' and resid 212 through 237 Proline residue: A 232 - end of helix Processing helix chain 'A' and resid 247 through 272 removed outlier: 4.190A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 287 through 307 removed outlier: 3.883A pdb=" N LEU A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 315 through 341 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 351 through 363 Processing helix chain 'A' and resid 368 through 400 Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'B' and resid 238 through 239 removed outlier: 3.703A pdb=" N ILE B 239 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE B 244 " --> pdb=" O ILE B 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'A' and resid 238 through 239 removed outlier: 3.703A pdb=" N ILE A 239 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 244 " --> pdb=" O ILE A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 441 hydrogen bonds defined for protein. 1311 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: 1.53 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1379 1.34 - 1.45: 1411 1.45 - 1.57: 3380 1.57 - 1.69: 12 1.69 - 1.81: 66 Bond restraints: 6248 Sorted by residual: bond pdb=" CB PRO A 115 " pdb=" CG PRO A 115 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.56e+00 bond pdb=" CB PRO B 115 " pdb=" CG PRO B 115 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.55e+00 bond pdb=" CA PRO A 108 " pdb=" C PRO A 108 " ideal model delta sigma weight residual 1.517 1.559 -0.042 1.54e-02 4.22e+03 7.49e+00 bond pdb=" CA PRO B 108 " pdb=" C PRO B 108 " ideal model delta sigma weight residual 1.517 1.558 -0.042 1.54e-02 4.22e+03 7.39e+00 bond pdb=" CB PRO B 108 " pdb=" CG PRO B 108 " ideal model delta sigma weight residual 1.492 1.612 -0.120 5.00e-02 4.00e+02 5.74e+00 ... (remaining 6243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 8287 3.79 - 7.58: 197 7.58 - 11.38: 26 11.38 - 15.17: 12 15.17 - 18.96: 2 Bond angle restraints: 8524 Sorted by residual: angle pdb=" CA PRO A 115 " pdb=" N PRO A 115 " pdb=" CD PRO A 115 " ideal model delta sigma weight residual 112.00 99.70 12.30 1.40e+00 5.10e-01 7.72e+01 angle pdb=" CA PRO B 115 " pdb=" N PRO B 115 " pdb=" CD PRO B 115 " ideal model delta sigma weight residual 112.00 99.71 12.29 1.40e+00 5.10e-01 7.71e+01 angle pdb=" CA PRO A 108 " pdb=" N PRO A 108 " pdb=" CD PRO A 108 " ideal model delta sigma weight residual 112.00 100.26 11.74 1.40e+00 5.10e-01 7.03e+01 angle pdb=" CA PRO B 108 " pdb=" N PRO B 108 " pdb=" CD PRO B 108 " ideal model delta sigma weight residual 112.00 100.28 11.72 1.40e+00 5.10e-01 7.01e+01 angle pdb=" CA LEU A 48 " pdb=" CB LEU A 48 " pdb=" CG LEU A 48 " ideal model delta sigma weight residual 116.30 135.26 -18.96 3.50e+00 8.16e-02 2.93e+01 ... (remaining 8519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 3182 16.52 - 33.04: 286 33.04 - 49.56: 98 49.56 - 66.08: 54 66.08 - 82.61: 14 Dihedral angle restraints: 3634 sinusoidal: 1426 harmonic: 2208 Sorted by residual: dihedral pdb=" C PRO B 108 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " pdb=" CB PRO B 108 " ideal model delta harmonic sigma weight residual -120.70 -129.60 8.90 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" C PRO A 108 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " pdb=" CB PRO A 108 " ideal model delta harmonic sigma weight residual -120.70 -129.55 8.85 0 2.50e+00 1.60e-01 1.25e+01 dihedral pdb=" CA ASP A 348 " pdb=" CB ASP A 348 " pdb=" CG ASP A 348 " pdb=" OD1 ASP A 348 " ideal model delta sinusoidal sigma weight residual -30.00 -89.32 59.32 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 3631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 758 0.081 - 0.162: 188 0.162 - 0.244: 30 0.244 - 0.325: 6 0.325 - 0.406: 2 Chirality restraints: 984 Sorted by residual: chirality pdb=" CA PRO B 108 " pdb=" N PRO B 108 " pdb=" C PRO B 108 " pdb=" CB PRO B 108 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA PRO A 108 " pdb=" N PRO A 108 " pdb=" C PRO A 108 " pdb=" CB PRO A 108 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB THR A 214 " pdb=" CA THR A 214 " pdb=" OG1 THR A 214 " pdb=" CG2 THR A 214 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 981 not shown) Planarity restraints: 1036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 114 " 0.103 5.00e-02 4.00e+02 1.45e-01 3.39e+01 pdb=" N PRO A 115 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 114 " 0.102 5.00e-02 4.00e+02 1.45e-01 3.37e+01 pdb=" N PRO B 115 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 107 " -0.094 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO A 108 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO A 108 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 108 " -0.071 5.00e-02 4.00e+02 ... (remaining 1033 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 38 2.59 - 3.17: 5029 3.17 - 3.74: 9890 3.74 - 4.32: 12054 4.32 - 4.90: 20504 Nonbonded interactions: 47515 Sorted by model distance: nonbonded pdb=" OD1 ASP B 154 " pdb="MG MG B 502 " model vdw 2.008 2.170 nonbonded pdb=" OD1 ASP A 154 " pdb="MG MG A 502 " model vdw 2.009 2.170 nonbonded pdb="MG MG B 502 " pdb=" O2B CDC B 503 " model vdw 2.085 2.170 nonbonded pdb="MG MG A 502 " pdb=" O2B CDC A 503 " model vdw 2.086 2.170 nonbonded pdb=" OD1 ASP A 180 " pdb=" OH TYR A 304 " model vdw 2.269 3.040 ... (remaining 47510 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' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.970 Find NCS groups from input model: 0.170 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.008 0.146 6248 Z= 0.534 Angle : 1.459 18.960 8524 Z= 0.833 Chirality : 0.077 0.406 984 Planarity : 0.015 0.199 1036 Dihedral : 16.780 82.606 2210 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.30 % Allowed : 19.94 % 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: 1.24 (0.29), residues: 756 helix: 0.99 (0.20), residues: 554 sheet: None (None), residues: 0 loop : 0.67 (0.47), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP B 181 HIS 0.007 0.002 HIS A 46 PHE 0.069 0.004 PHE B 234 TYR 0.047 0.006 TYR A 362 ARG 0.010 0.002 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 GLN cc_start: 0.8807 (mt0) cc_final: 0.8524 (mt0) REVERT: B 82 TRP cc_start: 0.8514 (p90) cc_final: 0.8297 (p90) REVERT: B 130 GLN cc_start: 0.8216 (tp40) cc_final: 0.7863 (tp-100) REVERT: B 344 MET cc_start: 0.7872 (mtp) cc_final: 0.7572 (mtt) REVERT: B 361 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8108 (mm-40) REVERT: A 82 TRP cc_start: 0.8500 (p90) cc_final: 0.8279 (p90) REVERT: A 130 GLN cc_start: 0.8265 (tp40) cc_final: 0.7914 (tp-100) REVERT: A 361 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8294 (mm-40) outliers start: 2 outliers final: 0 residues processed: 192 average time/residue: 0.1955 time to fit residues: 47.8365 Evaluate side-chains 172 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6248 Z= 0.196 Angle : 0.631 8.728 8524 Z= 0.330 Chirality : 0.042 0.132 984 Planarity : 0.005 0.051 1036 Dihedral : 7.521 52.373 874 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 4.08 % Allowed : 16.47 % Favored : 79.46 % 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: 2.74 (0.29), residues: 756 helix: 2.16 (0.20), residues: 558 sheet: None (None), residues: 0 loop : 0.99 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 117 HIS 0.004 0.001 HIS B 315 PHE 0.017 0.002 PHE B 358 TYR 0.012 0.002 TYR B 387 ARG 0.007 0.001 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 177 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8602 (mmm) REVERT: B 142 ARG cc_start: 0.8289 (tpt90) cc_final: 0.7931 (tpt90) REVERT: B 260 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8306 (t80) REVERT: A 142 ARG cc_start: 0.8355 (tpt90) cc_final: 0.7965 (tpt90) REVERT: A 184 PHE cc_start: 0.8443 (t80) cc_final: 0.8234 (t80) REVERT: A 260 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8305 (t80) outliers start: 27 outliers final: 16 residues processed: 191 average time/residue: 0.1942 time to fit residues: 47.3250 Evaluate side-chains 175 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 GLN A 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6248 Z= 0.196 Angle : 0.577 6.036 8524 Z= 0.302 Chirality : 0.041 0.146 984 Planarity : 0.004 0.036 1036 Dihedral : 6.131 46.250 874 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.23 % Allowed : 19.49 % Favored : 76.28 % 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: 2.99 (0.30), residues: 756 helix: 2.35 (0.20), residues: 560 sheet: None (None), residues: 0 loop : 1.03 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 117 HIS 0.004 0.001 HIS A 315 PHE 0.016 0.002 PHE B 187 TYR 0.011 0.001 TYR A 387 ARG 0.003 0.000 ARG A 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 ARG cc_start: 0.8385 (tpt90) cc_final: 0.8035 (tpt90) REVERT: B 193 PHE cc_start: 0.8055 (t80) cc_final: 0.7777 (t80) REVERT: B 260 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8202 (t80) REVERT: B 306 LYS cc_start: 0.8052 (tppt) cc_final: 0.7832 (tppt) REVERT: A 45 ARG cc_start: 0.7444 (ttt90) cc_final: 0.6932 (tmm160) REVERT: A 142 ARG cc_start: 0.8428 (tpt90) cc_final: 0.8048 (tpt90) REVERT: A 184 PHE cc_start: 0.8541 (t80) cc_final: 0.8293 (t80) REVERT: A 193 PHE cc_start: 0.8112 (t80) cc_final: 0.7826 (t80) REVERT: A 306 LYS cc_start: 0.8030 (tppt) cc_final: 0.7806 (tppt) outliers start: 28 outliers final: 21 residues processed: 175 average time/residue: 0.2190 time to fit residues: 49.7124 Evaluate side-chains 184 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 401 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 69 GLN A 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6248 Z= 0.194 Angle : 0.566 9.746 8524 Z= 0.294 Chirality : 0.041 0.142 984 Planarity : 0.004 0.038 1036 Dihedral : 5.904 44.822 874 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 5.44 % Allowed : 19.49 % Favored : 75.08 % 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: 2.96 (0.30), residues: 756 helix: 2.32 (0.20), residues: 560 sheet: None (None), residues: 0 loop : 1.04 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 117 HIS 0.004 0.001 HIS B 197 PHE 0.021 0.002 PHE B 234 TYR 0.018 0.001 TYR A 362 ARG 0.005 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 ARG cc_start: 0.8080 (mmt-90) cc_final: 0.7624 (tpp80) REVERT: B 57 GLN cc_start: 0.7660 (mm110) cc_final: 0.7336 (mp10) REVERT: B 119 TYR cc_start: 0.8253 (m-80) cc_final: 0.8018 (m-80) REVERT: B 141 ARG cc_start: 0.8309 (mmt-90) cc_final: 0.8064 (mpt-90) REVERT: B 174 GLN cc_start: 0.9126 (mt0) cc_final: 0.8605 (mt0) REVERT: B 260 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8136 (t80) REVERT: A 127 PHE cc_start: 0.8757 (t80) cc_final: 0.8531 (t80) REVERT: A 193 PHE cc_start: 0.8201 (t80) cc_final: 0.7867 (t80) REVERT: A 260 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8130 (t80) outliers start: 36 outliers final: 21 residues processed: 190 average time/residue: 0.2084 time to fit residues: 49.9866 Evaluate side-chains 190 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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: 0.7434 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6248 Z= 0.350 Angle : 0.683 10.331 8524 Z= 0.353 Chirality : 0.045 0.166 984 Planarity : 0.005 0.039 1036 Dihedral : 5.710 40.624 874 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 6.65 % Allowed : 21.75 % Favored : 71.60 % 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 (0.30), residues: 756 helix: 1.96 (0.20), residues: 558 sheet: None (None), residues: 0 loop : 1.20 (0.50), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 374 HIS 0.005 0.001 HIS B 197 PHE 0.016 0.002 PHE B 358 TYR 0.011 0.002 TYR B 201 ARG 0.005 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 177 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 ARG cc_start: 0.8220 (mmt-90) cc_final: 0.7857 (tpp80) REVERT: B 57 GLN cc_start: 0.7799 (mm110) cc_final: 0.7546 (mm-40) REVERT: B 98 CYS cc_start: 0.7826 (m) cc_final: 0.7365 (p) REVERT: B 127 PHE cc_start: 0.8813 (t80) cc_final: 0.8572 (t80) REVERT: B 174 GLN cc_start: 0.9184 (mt0) cc_final: 0.8425 (mt0) REVERT: B 260 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8130 (t80) REVERT: B 306 LYS cc_start: 0.7980 (tppt) cc_final: 0.7756 (tppt) REVERT: A 55 ARG cc_start: 0.8252 (tpp80) cc_final: 0.7935 (mpt-90) REVERT: A 98 CYS cc_start: 0.7807 (m) cc_final: 0.7383 (p) REVERT: A 127 PHE cc_start: 0.8849 (t80) cc_final: 0.8584 (t80) REVERT: A 174 GLN cc_start: 0.9204 (mt0) cc_final: 0.8523 (mt0) REVERT: A 182 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8154 (ttp) REVERT: A 260 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8152 (t80) REVERT: A 306 LYS cc_start: 0.8038 (tppt) cc_final: 0.7746 (tppt) outliers start: 44 outliers final: 33 residues processed: 197 average time/residue: 0.1945 time to fit residues: 48.8181 Evaluate side-chains 205 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 392 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6248 Z= 0.200 Angle : 0.605 11.462 8524 Z= 0.308 Chirality : 0.041 0.125 984 Planarity : 0.004 0.039 1036 Dihedral : 5.636 40.252 874 Min Nonbonded Distance : 1.407 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 5.29 % Allowed : 25.98 % Favored : 68.73 % 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: 2.71 (0.30), residues: 756 helix: 2.09 (0.21), residues: 560 sheet: None (None), residues: 0 loop : 1.11 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 235 HIS 0.004 0.001 HIS B 197 PHE 0.021 0.002 PHE A 234 TYR 0.017 0.002 TYR A 129 ARG 0.004 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLN cc_start: 0.7731 (mm110) cc_final: 0.7508 (mm-40) REVERT: B 61 ARG cc_start: 0.7394 (mtp-110) cc_final: 0.6944 (mtp-110) REVERT: B 127 PHE cc_start: 0.8769 (t80) cc_final: 0.8521 (t80) REVERT: B 142 ARG cc_start: 0.8857 (tpp80) cc_final: 0.8622 (tpt90) REVERT: B 174 GLN cc_start: 0.9113 (mt0) cc_final: 0.8634 (mt0) REVERT: B 182 MET cc_start: 0.8473 (tpp) cc_final: 0.8249 (tpp) REVERT: B 260 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8119 (t80) REVERT: B 302 MET cc_start: 0.8567 (mmt) cc_final: 0.8031 (mmt) REVERT: B 306 LYS cc_start: 0.7966 (tppt) cc_final: 0.7754 (tppt) REVERT: B 367 ILE cc_start: 0.8261 (mm) cc_final: 0.7994 (tt) REVERT: A 61 ARG cc_start: 0.7045 (mtp-110) cc_final: 0.6806 (mtp-110) REVERT: A 127 PHE cc_start: 0.8828 (t80) cc_final: 0.8590 (t80) REVERT: A 174 GLN cc_start: 0.9131 (mt0) cc_final: 0.8567 (mt0) REVERT: A 182 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8134 (ttp) REVERT: A 260 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8137 (t80) REVERT: A 302 MET cc_start: 0.8592 (mmt) cc_final: 0.8105 (mmt) REVERT: A 367 ILE cc_start: 0.8234 (mm) cc_final: 0.7960 (tt) outliers start: 35 outliers final: 26 residues processed: 203 average time/residue: 0.1949 time to fit residues: 50.0920 Evaluate side-chains 206 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 177 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7351 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6248 Z= 0.194 Angle : 0.627 11.969 8524 Z= 0.312 Chirality : 0.041 0.130 984 Planarity : 0.004 0.038 1036 Dihedral : 5.495 39.157 874 Min Nonbonded Distance : 1.301 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.53 % Allowed : 28.25 % Favored : 67.22 % 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: 2.65 (0.30), residues: 756 helix: 2.05 (0.21), residues: 572 sheet: None (None), residues: 0 loop : 1.02 (0.51), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 235 HIS 0.003 0.001 HIS B 197 PHE 0.013 0.001 PHE B 187 TYR 0.019 0.002 TYR A 129 ARG 0.002 0.000 ARG B 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 ARG cc_start: 0.8284 (mpt-90) cc_final: 0.7978 (mmt-90) REVERT: B 57 GLN cc_start: 0.7801 (mm110) cc_final: 0.7599 (mm-40) REVERT: B 182 MET cc_start: 0.8431 (tpp) cc_final: 0.8201 (tpp) REVERT: B 260 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8058 (t80) REVERT: B 302 MET cc_start: 0.8548 (mmt) cc_final: 0.8146 (mmm) REVERT: B 306 LYS cc_start: 0.7976 (tppt) cc_final: 0.7737 (tppt) REVERT: A 127 PHE cc_start: 0.8838 (t80) cc_final: 0.8599 (t80) REVERT: A 182 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7941 (ttp) REVERT: A 260 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8067 (t80) REVERT: A 302 MET cc_start: 0.8528 (mmt) cc_final: 0.8097 (mmt) REVERT: A 367 ILE cc_start: 0.8232 (mm) cc_final: 0.8013 (tp) REVERT: A 368 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7320 (m-30) outliers start: 30 outliers final: 23 residues processed: 199 average time/residue: 0.2175 time to fit residues: 55.7775 Evaluate side-chains 206 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 66 optimal weight: 0.0170 chunk 70 optimal weight: 0.6980 chunk 64 optimal weight: 0.0000 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 overall best weight: 0.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 GLN A 130 GLN A 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6248 Z= 0.199 Angle : 0.659 12.499 8524 Z= 0.321 Chirality : 0.040 0.130 984 Planarity : 0.004 0.038 1036 Dihedral : 5.548 39.894 874 Min Nonbonded Distance : 1.295 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.23 % Allowed : 30.06 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.59 (0.30), residues: 756 helix: 2.01 (0.21), residues: 572 sheet: None (None), residues: 0 loop : 0.97 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 82 HIS 0.006 0.001 HIS B 402 PHE 0.021 0.001 PHE A 234 TYR 0.019 0.002 TYR A 362 ARG 0.004 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 ARG cc_start: 0.8166 (mpt-90) cc_final: 0.7865 (mmt-90) REVERT: B 61 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.6800 (mtp-110) REVERT: B 141 ARG cc_start: 0.8655 (mmt-90) cc_final: 0.8321 (mmt90) REVERT: B 260 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.7968 (t80) REVERT: B 306 LYS cc_start: 0.7881 (tppt) cc_final: 0.7015 (mmtt) REVERT: A 127 PHE cc_start: 0.8886 (t80) cc_final: 0.8656 (t80) REVERT: A 130 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7763 (tp-100) REVERT: A 153 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: A 190 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.7273 (p) REVERT: A 260 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8034 (t80) outliers start: 28 outliers final: 21 residues processed: 186 average time/residue: 0.1649 time to fit residues: 38.9639 Evaluate side-chains 193 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 64 optimal weight: 0.0970 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6248 Z= 0.198 Angle : 0.671 12.903 8524 Z= 0.327 Chirality : 0.041 0.133 984 Planarity : 0.004 0.038 1036 Dihedral : 5.553 40.596 874 Min Nonbonded Distance : 1.224 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.38 % Allowed : 30.06 % Favored : 65.56 % 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 (0.30), residues: 756 helix: 2.03 (0.21), residues: 574 sheet: None (None), residues: 0 loop : 0.84 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 181 HIS 0.003 0.001 HIS B 197 PHE 0.019 0.001 PHE B 249 TYR 0.024 0.002 TYR A 129 ARG 0.004 0.000 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 ARG cc_start: 0.8313 (mpt-90) cc_final: 0.8054 (mmt-90) REVERT: B 57 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7682 (mp10) REVERT: B 61 ARG cc_start: 0.7698 (mmm-85) cc_final: 0.6645 (mtp-110) REVERT: B 141 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.8282 (mmt90) REVERT: B 260 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7992 (t80) REVERT: B 306 LYS cc_start: 0.7812 (tppt) cc_final: 0.7084 (mmtt) REVERT: A 153 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: A 190 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.7256 (p) REVERT: A 260 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8062 (t80) outliers start: 29 outliers final: 21 residues processed: 179 average time/residue: 0.2003 time to fit residues: 45.5604 Evaluate side-chains 192 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 170 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 0.0670 chunk 8 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6248 Z= 0.201 Angle : 0.681 12.995 8524 Z= 0.334 Chirality : 0.041 0.149 984 Planarity : 0.004 0.038 1036 Dihedral : 5.584 41.562 874 Min Nonbonded Distance : 1.184 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.93 % Allowed : 31.12 % Favored : 64.95 % 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: 2.59 (0.30), residues: 756 helix: 2.08 (0.21), residues: 564 sheet: None (None), residues: 0 loop : 0.78 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 117 HIS 0.004 0.001 HIS B 197 PHE 0.014 0.001 PHE A 358 TYR 0.021 0.002 TYR A 362 ARG 0.007 0.001 ARG A 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 55 ARG cc_start: 0.8300 (mpt-90) cc_final: 0.8041 (mmt-90) REVERT: B 57 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7518 (mp10) REVERT: B 61 ARG cc_start: 0.7686 (mmm-85) cc_final: 0.7388 (mtp-110) REVERT: B 141 ARG cc_start: 0.8609 (mmt-90) cc_final: 0.8363 (mmt90) REVERT: B 153 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: B 260 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8004 (t80) REVERT: B 306 LYS cc_start: 0.7797 (tppt) cc_final: 0.7081 (mmtt) REVERT: A 153 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: A 260 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8037 (t80) REVERT: A 302 MET cc_start: 0.8552 (mmt) cc_final: 0.8106 (mtp) outliers start: 26 outliers final: 21 residues processed: 176 average time/residue: 0.2055 time to fit residues: 45.6210 Evaluate side-chains 191 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 153 PHE Chi-restraints excluded: chain B residue 170 CYS Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 253 CYS Chi-restraints excluded: chain B residue 260 PHE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 388 CYS Chi-restraints excluded: chain B residue 390 SER Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 PHE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 390 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.175048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136291 restraints weight = 8274.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141589 restraints weight = 4584.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.145118 restraints weight = 3079.167| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6248 Z= 0.228 Angle : 0.688 13.137 8524 Z= 0.338 Chirality : 0.042 0.177 984 Planarity : 0.004 0.039 1036 Dihedral : 5.525 41.764 874 Min Nonbonded Distance : 1.174 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.93 % Allowed : 30.51 % Favored : 65.56 % 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: 2.54 (0.30), residues: 756 helix: 2.04 (0.21), residues: 564 sheet: None (None), residues: 0 loop : 0.76 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 117 HIS 0.004 0.001 HIS B 197 PHE 0.014 0.001 PHE A 358 TYR 0.021 0.002 TYR A 362 ARG 0.005 0.000 ARG B 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1622.63 seconds wall clock time: 36 minutes 47.31 seconds (2207.31 seconds total)