Starting phenix.real_space_refine on Mon Mar 11 00:19:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urg_26712/03_2024/7urg_26712_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urg_26712/03_2024/7urg_26712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urg_26712/03_2024/7urg_26712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urg_26712/03_2024/7urg_26712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urg_26712/03_2024/7urg_26712_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urg_26712/03_2024/7urg_26712_neut_updated.pdb" } resolution = 3.46 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= -0.019 sd= 0.302 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 28 5.16 5 C 3934 2.51 5 N 1082 2.21 5 O 1210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 165": "OD1" <-> "OD2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6260 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3101 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 17, 'TRANS': 383} Chain: "B" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3101 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 17, 'TRANS': 383} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'TTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'TTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.97, per 1000 atoms: 0.63 Number of scatterers: 6260 At special positions: 0 Unit cell: (138.03, 69.55, 66.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 6 15.00 O 1210 8.00 N 1082 7.00 C 3934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 196 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.92 Conformation dependent library (CDL) restraints added in 1.2 seconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1448 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 8 sheets defined 39.7% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 removed outlier: 3.674A pdb=" N TYR A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 102 removed outlier: 3.858A pdb=" N LYS A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 151 through 162 Processing helix chain 'A' and resid 211 through 228 removed outlier: 4.233A pdb=" N GLY A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 removed outlier: 3.690A pdb=" N SER A 234 " --> pdb=" O VAL A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 264 through 276 Processing helix chain 'A' and resid 284 through 306 Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 364 through 367 No H-bonds generated for 'chain 'A' and resid 364 through 367' Processing helix chain 'A' and resid 369 through 386 removed outlier: 4.282A pdb=" N THR A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.675A pdb=" N TYR B 58 " --> pdb=" O HIS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 102 removed outlier: 3.859A pdb=" N LYS B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'B' and resid 151 through 162 Processing helix chain 'B' and resid 211 through 228 removed outlier: 4.233A pdb=" N GLY B 227 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 234 removed outlier: 3.690A pdb=" N SER B 234 " --> pdb=" O VAL B 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 231 through 234' Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 264 through 276 Processing helix chain 'B' and resid 284 through 306 Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 364 through 367 No H-bonds generated for 'chain 'B' and resid 364 through 367' Processing helix chain 'B' and resid 369 through 386 removed outlier: 4.281A pdb=" N THR B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 413 Processing sheet with id= A, first strand: chain 'A' and resid 30 through 34 removed outlier: 6.528A pdb=" N GLY A 61 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE A 33 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ALA A 63 " --> pdb=" O PHE A 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 111 through 115 removed outlier: 7.175A pdb=" N LYS A 136 " --> pdb=" O CYS A 112 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU A 114 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS A 138 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 198 through 202 removed outlier: 6.415A pdb=" N GLY A 247 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL A 201 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY A 249 " --> pdb=" O VAL A 201 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 343 through 348 Processing sheet with id= E, first strand: chain 'B' and resid 30 through 34 removed outlier: 6.527A pdb=" N GLY B 61 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE B 33 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ALA B 63 " --> pdb=" O PHE B 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 111 through 115 removed outlier: 7.175A pdb=" N LYS B 136 " --> pdb=" O CYS B 112 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LEU B 114 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N CYS B 138 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 198 through 202 removed outlier: 6.415A pdb=" N GLY B 247 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL B 201 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY B 249 " --> pdb=" O VAL B 201 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 343 through 348 208 hydrogen bonds defined for protein. 618 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: 1.54 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2086 1.35 - 1.46: 1491 1.46 - 1.58: 2773 1.58 - 1.70: 10 1.70 - 1.82: 38 Bond restraints: 6398 Sorted by residual: bond pdb=" CG GLU B 187 " pdb=" CD GLU B 187 " ideal model delta sigma weight residual 1.516 1.498 0.018 2.50e-02 1.60e+03 5.09e-01 bond pdb=" CG GLU A 187 " pdb=" CD GLU A 187 " ideal model delta sigma weight residual 1.516 1.498 0.018 2.50e-02 1.60e+03 4.96e-01 bond pdb=" C LEU B 80 " pdb=" N VAL B 81 " ideal model delta sigma weight residual 1.332 1.325 0.006 9.20e-03 1.18e+04 4.81e-01 bond pdb=" CA VAL B 246 " pdb=" CB VAL B 246 " ideal model delta sigma weight residual 1.540 1.549 -0.009 1.36e-02 5.41e+03 4.25e-01 bond pdb=" CA VAL A 246 " pdb=" CB VAL A 246 " ideal model delta sigma weight residual 1.540 1.549 -0.009 1.36e-02 5.41e+03 4.25e-01 ... (remaining 6393 not shown) Histogram of bond angle deviations from ideal: 100.94 - 107.55: 250 107.55 - 114.17: 3581 114.17 - 120.79: 2740 120.79 - 127.40: 2051 127.40 - 134.02: 80 Bond angle restraints: 8702 Sorted by residual: angle pdb=" CA GLU B 97 " pdb=" CB GLU B 97 " pdb=" CG GLU B 97 " ideal model delta sigma weight residual 114.10 118.03 -3.93 2.00e+00 2.50e-01 3.87e+00 angle pdb=" CA GLU A 97 " pdb=" CB GLU A 97 " pdb=" CG GLU A 97 " ideal model delta sigma weight residual 114.10 117.99 -3.89 2.00e+00 2.50e-01 3.78e+00 angle pdb=" C LEU A 186 " pdb=" CA LEU A 186 " pdb=" CB LEU A 186 " ideal model delta sigma weight residual 110.35 106.67 3.68 1.91e+00 2.74e-01 3.72e+00 angle pdb=" C LEU B 186 " pdb=" CA LEU B 186 " pdb=" CB LEU B 186 " ideal model delta sigma weight residual 110.35 106.69 3.66 1.91e+00 2.74e-01 3.67e+00 angle pdb=" C2' TTP A 801 " pdb=" C3' TTP A 801 " pdb=" C4' TTP A 801 " ideal model delta sigma weight residual 111.00 105.26 5.74 3.00e+00 1.11e-01 3.66e+00 ... (remaining 8697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 3522 23.43 - 46.86: 202 46.86 - 70.29: 44 70.29 - 93.72: 6 93.72 - 117.15: 4 Dihedral angle restraints: 3778 sinusoidal: 1496 harmonic: 2282 Sorted by residual: dihedral pdb=" CB CYS A 30 " pdb=" SG CYS A 30 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -174.64 88.64 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS B 30 " pdb=" SG CYS B 30 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual -86.00 -174.59 88.59 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual -58.32 -175.47 117.15 1 2.00e+01 2.50e-03 3.50e+01 ... (remaining 3775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 593 0.025 - 0.051: 220 0.051 - 0.076: 70 0.076 - 0.102: 44 0.102 - 0.127: 27 Chirality restraints: 954 Sorted by residual: chirality pdb=" CA VAL A 201 " pdb=" N VAL A 201 " pdb=" C VAL A 201 " pdb=" CB VAL A 201 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA ILE B 166 " pdb=" N ILE B 166 " pdb=" C ILE B 166 " pdb=" CB ILE B 166 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA ILE B 314 " pdb=" N ILE B 314 " pdb=" C ILE B 314 " pdb=" CB ILE B 314 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 951 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 26 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO B 27 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 27 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 27 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 27 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 97 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C GLU A 97 " 0.017 2.00e-02 2.50e+03 pdb=" O GLU A 97 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE A 98 " -0.006 2.00e-02 2.50e+03 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1082 2.76 - 3.30: 6096 3.30 - 3.83: 9961 3.83 - 4.37: 11322 4.37 - 4.90: 20115 Nonbonded interactions: 48576 Sorted by model distance: nonbonded pdb=" O LEU A 99 " pdb=" N GLY A 103 " model vdw 2.229 2.520 nonbonded pdb=" O LEU B 99 " pdb=" N GLY B 103 " model vdw 2.229 2.520 nonbonded pdb=" ND2 ASN A 96 " pdb=" O TRP A 134 " model vdw 2.232 2.520 nonbonded pdb=" ND2 ASN B 96 " pdb=" O TRP B 134 " model vdw 2.233 2.520 nonbonded pdb=" O ILE B 45 " pdb=" OG SER B 48 " model vdw 2.264 2.440 ... (remaining 48571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 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: 2.580 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: 3.890 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.330 Find NCS groups from input model: 0.290 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 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 : 0.002 0.018 6398 Z= 0.146 Angle : 0.499 5.927 8702 Z= 0.255 Chirality : 0.038 0.127 954 Planarity : 0.003 0.030 1122 Dihedral : 15.443 117.149 2324 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 13.29 % Favored : 86.71 % 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: 0.73 (0.31), residues: 798 helix: 2.52 (0.30), residues: 322 sheet: -0.69 (0.52), residues: 110 loop : -1.05 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 369 HIS 0.003 0.001 HIS A 390 PHE 0.006 0.001 PHE B 124 TYR 0.006 0.001 TYR A 264 ARG 0.001 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7172 (tmm-80) REVERT: B 100 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7166 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2401 time to fit residues: 22.7660 Evaluate side-chains 67 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN A 390 HIS B 176 ASN B 390 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 6398 Z= 0.548 Angle : 0.768 11.451 8702 Z= 0.388 Chirality : 0.048 0.158 954 Planarity : 0.005 0.030 1122 Dihedral : 10.660 142.510 906 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.32 % Allowed : 14.35 % Favored : 82.33 % 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: -0.46 (0.30), residues: 798 helix: 1.71 (0.29), residues: 310 sheet: -1.46 (0.47), residues: 130 loop : -1.72 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP A 49 HIS 0.013 0.003 HIS A 390 PHE 0.021 0.003 PHE B 394 TYR 0.016 0.002 TYR B 421 ARG 0.004 0.001 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.5652 (mp0) REVERT: B 148 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.5592 (mp0) outliers start: 22 outliers final: 8 residues processed: 84 average time/residue: 0.2517 time to fit residues: 26.6790 Evaluate side-chains 58 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 331 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7319 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6398 Z= 0.182 Angle : 0.531 6.112 8702 Z= 0.268 Chirality : 0.040 0.123 954 Planarity : 0.003 0.031 1122 Dihedral : 10.199 144.851 906 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.87 % Allowed : 15.41 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.30), residues: 798 helix: 1.87 (0.29), residues: 322 sheet: -0.56 (0.56), residues: 96 loop : -1.50 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 369 HIS 0.003 0.001 HIS A 226 PHE 0.010 0.001 PHE B 124 TYR 0.007 0.001 TYR B 264 ARG 0.002 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 53 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5334 (mp0) REVERT: A 322 TYR cc_start: 0.7106 (m-80) cc_final: 0.6829 (m-80) REVERT: B 148 GLU cc_start: 0.6181 (OUTLIER) cc_final: 0.5336 (mp0) outliers start: 19 outliers final: 14 residues processed: 68 average time/residue: 0.2163 time to fit residues: 19.2534 Evaluate side-chains 64 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 251 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6398 Z= 0.236 Angle : 0.543 6.003 8702 Z= 0.275 Chirality : 0.041 0.131 954 Planarity : 0.003 0.030 1122 Dihedral : 10.452 153.523 906 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.53 % Allowed : 15.26 % Favored : 80.21 % 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: -0.09 (0.31), residues: 798 helix: 2.03 (0.29), residues: 310 sheet: -1.43 (0.47), residues: 130 loop : -1.43 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 411 HIS 0.003 0.001 HIS A 54 PHE 0.011 0.001 PHE B 124 TYR 0.008 0.001 TYR B 105 ARG 0.001 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 54 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5215 (mp0) REVERT: A 187 GLU cc_start: 0.8642 (pm20) cc_final: 0.7388 (pm20) REVERT: A 228 LYS cc_start: 0.5899 (mmtm) cc_final: 0.5181 (mmmm) REVERT: B 148 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5219 (mp0) REVERT: B 187 GLU cc_start: 0.8638 (pm20) cc_final: 0.7386 (pm20) REVERT: B 322 TYR cc_start: 0.7115 (m-10) cc_final: 0.6763 (m-10) outliers start: 30 outliers final: 24 residues processed: 82 average time/residue: 0.1755 time to fit residues: 19.4923 Evaluate side-chains 76 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 50 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.4100 ------------------------------------------------------------------------------- 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: 0.7274 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 6398 Z= 0.122 Angle : 0.472 7.394 8702 Z= 0.233 Chirality : 0.038 0.117 954 Planarity : 0.003 0.029 1122 Dihedral : 9.900 148.749 906 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.02 % Allowed : 16.01 % Favored : 80.97 % 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: 0.25 (0.31), residues: 798 helix: 1.95 (0.29), residues: 330 sheet: -0.45 (0.57), residues: 96 loop : -1.37 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 369 HIS 0.001 0.001 HIS B 200 PHE 0.008 0.001 PHE B 124 TYR 0.012 0.001 TYR B 322 ARG 0.002 0.000 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8562 (pm20) cc_final: 0.7460 (pm20) REVERT: B 187 GLU cc_start: 0.8539 (pm20) cc_final: 0.7430 (pm20) outliers start: 20 outliers final: 18 residues processed: 77 average time/residue: 0.2197 time to fit residues: 22.3703 Evaluate side-chains 75 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 45 optimal weight: 0.0070 chunk 19 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.0050 chunk 40 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6012 ------------------------------------------------------------------------------- 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: 0.7296 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 6398 Z= 0.145 Angle : 0.479 6.633 8702 Z= 0.238 Chirality : 0.039 0.117 954 Planarity : 0.003 0.026 1122 Dihedral : 9.776 147.780 906 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.02 % Allowed : 15.86 % Favored : 81.12 % 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: 0.30 (0.31), residues: 798 helix: 2.13 (0.29), residues: 320 sheet: -1.00 (0.49), residues: 126 loop : -1.19 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 369 HIS 0.002 0.001 HIS B 54 PHE 0.009 0.001 PHE A 124 TYR 0.007 0.001 TYR B 322 ARG 0.001 0.000 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8643 (pm20) cc_final: 0.7890 (pm20) REVERT: A 264 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.8546 (m-80) REVERT: B 187 GLU cc_start: 0.8638 (pm20) cc_final: 0.7886 (pm20) REVERT: B 264 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8552 (m-80) outliers start: 20 outliers final: 16 residues processed: 76 average time/residue: 0.1747 time to fit residues: 18.0936 Evaluate side-chains 75 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 57 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.0870 chunk 77 optimal weight: 0.0970 chunk 48 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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: 0.7273 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6398 Z= 0.129 Angle : 0.457 6.344 8702 Z= 0.227 Chirality : 0.039 0.115 954 Planarity : 0.003 0.027 1122 Dihedral : 9.573 146.806 906 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.32 % Allowed : 15.86 % Favored : 80.82 % 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: 0.46 (0.31), residues: 798 helix: 2.24 (0.29), residues: 320 sheet: -0.78 (0.52), residues: 114 loop : -1.13 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 369 HIS 0.002 0.001 HIS B 54 PHE 0.009 0.001 PHE B 124 TYR 0.005 0.001 TYR B 372 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 61 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8600 (pm20) cc_final: 0.7904 (pm20) REVERT: B 187 GLU cc_start: 0.8588 (pm20) cc_final: 0.7892 (pm20) outliers start: 22 outliers final: 20 residues processed: 79 average time/residue: 0.1919 time to fit residues: 20.3915 Evaluate side-chains 76 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 56 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: 0.7332 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6398 Z= 0.213 Angle : 0.505 6.254 8702 Z= 0.255 Chirality : 0.040 0.121 954 Planarity : 0.003 0.054 1122 Dihedral : 9.765 146.874 906 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.17 % Allowed : 17.07 % 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: 0.25 (0.31), residues: 798 helix: 2.16 (0.29), residues: 314 sheet: -1.10 (0.49), residues: 130 loop : -1.19 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 167 HIS 0.003 0.001 HIS B 226 PHE 0.010 0.001 PHE B 124 TYR 0.007 0.001 TYR A 105 ARG 0.010 0.000 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 57 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 180 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8780 (tt) REVERT: A 187 GLU cc_start: 0.8683 (pm20) cc_final: 0.8029 (pm20) REVERT: A 228 LYS cc_start: 0.6189 (mmtm) cc_final: 0.5660 (mmmm) REVERT: A 308 MET cc_start: 0.8008 (mmm) cc_final: 0.7340 (mmm) REVERT: B 187 GLU cc_start: 0.8672 (pm20) cc_final: 0.8070 (pm20) REVERT: B 308 MET cc_start: 0.8056 (mmm) cc_final: 0.7430 (mmm) REVERT: B 424 GLN cc_start: 0.8265 (mp10) cc_final: 0.7856 (mp10) outliers start: 21 outliers final: 20 residues processed: 74 average time/residue: 0.1833 time to fit residues: 18.3009 Evaluate side-chains 78 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 57 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 75 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7310 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6398 Z= 0.170 Angle : 0.472 6.043 8702 Z= 0.237 Chirality : 0.039 0.118 954 Planarity : 0.003 0.055 1122 Dihedral : 9.764 150.171 906 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.47 % Allowed : 16.62 % Favored : 79.91 % 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: 0.29 (0.31), residues: 798 helix: 2.14 (0.29), residues: 320 sheet: -1.14 (0.49), residues: 130 loop : -1.14 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 146 HIS 0.003 0.001 HIS B 54 PHE 0.009 0.001 PHE A 124 TYR 0.006 0.001 TYR B 372 ARG 0.013 0.000 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 56 time to evaluate : 0.719 Fit side-chains REVERT: A 187 GLU cc_start: 0.8653 (pm20) cc_final: 0.8000 (pm20) REVERT: A 228 LYS cc_start: 0.5914 (mmtm) cc_final: 0.5608 (mmmm) REVERT: A 308 MET cc_start: 0.7966 (mmm) cc_final: 0.7396 (mmm) REVERT: B 180 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8789 (tt) REVERT: B 187 GLU cc_start: 0.8640 (pm20) cc_final: 0.8037 (pm20) REVERT: B 308 MET cc_start: 0.8003 (mmm) cc_final: 0.7385 (mmm) REVERT: B 424 GLN cc_start: 0.8231 (mp10) cc_final: 0.7847 (mp10) outliers start: 23 outliers final: 20 residues processed: 75 average time/residue: 0.1696 time to fit residues: 17.6515 Evaluate side-chains 76 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 55 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.7355 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6398 Z= 0.234 Angle : 0.508 6.093 8702 Z= 0.258 Chirality : 0.040 0.121 954 Planarity : 0.003 0.045 1122 Dihedral : 10.098 152.729 906 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.17 % Allowed : 17.07 % 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: 0.10 (0.31), residues: 798 helix: 2.14 (0.29), residues: 312 sheet: -1.27 (0.49), residues: 130 loop : -1.33 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 146 HIS 0.003 0.001 HIS A 54 PHE 0.010 0.001 PHE A 124 TYR 0.008 0.001 TYR A 105 ARG 0.013 0.000 ARG B 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 51 time to evaluate : 0.700 Fit side-chains REVERT: A 187 GLU cc_start: 0.8652 (pm20) cc_final: 0.8057 (pm20) REVERT: A 228 LYS cc_start: 0.5826 (mmtm) cc_final: 0.5563 (mmmm) REVERT: B 424 GLN cc_start: 0.8186 (mp10) cc_final: 0.7796 (mp10) outliers start: 21 outliers final: 21 residues processed: 72 average time/residue: 0.2212 time to fit residues: 21.0438 Evaluate side-chains 69 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 48 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 386 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4295 r_free = 0.4295 target = 0.204574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.170391 restraints weight = 6494.625| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.78 r_work: 0.3704 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6398 Z= 0.218 Angle : 0.504 5.935 8702 Z= 0.255 Chirality : 0.040 0.122 954 Planarity : 0.003 0.040 1122 Dihedral : 10.213 155.683 906 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.47 % Allowed : 17.37 % Favored : 79.15 % 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: 0.12 (0.31), residues: 798 helix: 2.11 (0.29), residues: 312 sheet: -1.18 (0.50), residues: 126 loop : -1.30 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 146 HIS 0.003 0.001 HIS B 54 PHE 0.010 0.001 PHE B 124 TYR 0.007 0.001 TYR B 105 ARG 0.011 0.000 ARG B 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1465.31 seconds wall clock time: 27 minutes 25.03 seconds (1645.03 seconds total)