Starting phenix.real_space_refine on Fri Aug 2 23:10:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4q_42975/08_2024/8v4q_42975.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4q_42975/08_2024/8v4q_42975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4q_42975/08_2024/8v4q_42975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4q_42975/08_2024/8v4q_42975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4q_42975/08_2024/8v4q_42975.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4q_42975/08_2024/8v4q_42975.cif" } resolution = 2.71 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= 0.002 sd= 0.047 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3782 2.51 5 N 1081 2.21 5 O 1104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 154": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5993 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2048 Classifications: {'peptide': 260} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 248} Chain breaks: 1 Chain: "B" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2092 Classifications: {'peptide': 266} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 254} Chain breaks: 1 Chain: "C" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1853 Classifications: {'peptide': 235} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 224} Chain breaks: 1 Time building chain proxies: 4.88, per 1000 atoms: 0.81 Number of scatterers: 5993 At special positions: 0 Unit cell: (117.914, 85.8346, 105.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1104 8.00 N 1081 7.00 C 3782 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 - 3.50 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: 2.01 Conformation dependent library (CDL) restraints added in 1.3 seconds 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 37.6% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 13 through 32 removed outlier: 3.567A pdb=" N ARG A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.607A pdb=" N ILE A 37 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 111 through 132 Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.734A pdb=" N GLN A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 203 through 210 removed outlier: 3.827A pdb=" N THR A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'B' and resid 13 through 30 removed outlier: 3.602A pdb=" N ARG B 30 " --> pdb=" O GLN B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 32 No H-bonds generated for 'chain 'B' and resid 31 through 32' Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 95 through 106 Processing helix chain 'B' and resid 111 through 132 removed outlier: 3.575A pdb=" N ALA B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 174 Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 203 through 210 removed outlier: 3.694A pdb=" N THR B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 273 No H-bonds generated for 'chain 'B' and resid 271 through 273' Processing helix chain 'C' and resid 13 through 30 removed outlier: 3.691A pdb=" N ARG C 30 " --> pdb=" O GLN C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 32 No H-bonds generated for 'chain 'C' and resid 31 through 32' Processing helix chain 'C' and resid 33 through 37 removed outlier: 3.745A pdb=" N ILE C 37 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 Processing helix chain 'C' and resid 111 through 132 Processing helix chain 'C' and resid 159 through 175 removed outlier: 3.755A pdb=" N GLN C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 193 Processing helix chain 'C' and resid 203 through 212 removed outlier: 3.515A pdb=" N THR C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C 211 " --> pdb=" O THR C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.600A pdb=" N ALA A 264 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASP A 244 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU A 262 " --> pdb=" O ASP A 244 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A 246 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG A 260 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ALA A 248 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.829A pdb=" N LEU A 148 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY A 227 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY A 215 " --> pdb=" O TYR A 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 41 removed outlier: 5.673A pdb=" N LEU B 239 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARG B 268 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL B 241 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU B 266 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET B 245 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU B 262 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 247 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG B 260 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR B 249 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 150 removed outlier: 4.332A pdb=" N GLY B 227 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 94 removed outlier: 5.220A pdb=" N ALA C 264 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASP C 244 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N LEU C 266 " --> pdb=" O SER C 242 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N SER C 242 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ARG C 268 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA C 240 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 148 through 150 removed outlier: 6.878A pdb=" N LEU C 148 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY C 227 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY C 215 " --> pdb=" O TYR C 181 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 732 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: 1.51 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1609 1.33 - 1.45: 1074 1.45 - 1.57: 3389 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 6118 Sorted by residual: bond pdb=" N LEU B 222 " pdb=" CA LEU B 222 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.27e-02 6.20e+03 7.88e+00 bond pdb=" N ARG C 36 " pdb=" CA ARG C 36 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.33e-02 5.65e+03 7.26e+00 bond pdb=" N THR A 104 " pdb=" CA THR A 104 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.90e+00 bond pdb=" N HIS A 105 " pdb=" CA HIS A 105 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.66e+00 bond pdb=" N ILE C 196 " pdb=" CA ILE C 196 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.24e-02 6.50e+03 5.44e+00 ... (remaining 6113 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.20: 221 107.20 - 113.95: 3377 113.95 - 120.70: 2515 120.70 - 127.45: 2114 127.45 - 134.20: 67 Bond angle restraints: 8294 Sorted by residual: angle pdb=" CA PHE C 178 " pdb=" CB PHE C 178 " pdb=" CG PHE C 178 " ideal model delta sigma weight residual 113.80 117.33 -3.53 1.00e+00 1.00e+00 1.24e+01 angle pdb=" C PHE C 178 " pdb=" CA PHE C 178 " pdb=" CB PHE C 178 " ideal model delta sigma weight residual 111.82 107.18 4.64 1.38e+00 5.25e-01 1.13e+01 angle pdb=" CA HIS A 105 " pdb=" C HIS A 105 " pdb=" O HIS A 105 " ideal model delta sigma weight residual 120.55 117.11 3.44 1.06e+00 8.90e-01 1.05e+01 angle pdb=" N TRP B 17 " pdb=" CA TRP B 17 " pdb=" C TRP B 17 " ideal model delta sigma weight residual 111.36 107.87 3.49 1.09e+00 8.42e-01 1.02e+01 angle pdb=" N ARG B 223 " pdb=" CA ARG B 223 " pdb=" CB ARG B 223 " ideal model delta sigma weight residual 110.69 105.73 4.96 1.61e+00 3.86e-01 9.51e+00 ... (remaining 8289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 3328 17.75 - 35.50: 266 35.50 - 53.25: 42 53.25 - 71.00: 14 71.00 - 88.75: 5 Dihedral angle restraints: 3655 sinusoidal: 1471 harmonic: 2184 Sorted by residual: dihedral pdb=" CA ASP A 154 " pdb=" CB ASP A 154 " pdb=" CG ASP A 154 " pdb=" OD1 ASP A 154 " ideal model delta sinusoidal sigma weight residual -30.00 -87.88 57.88 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CG ARG C 35 " pdb=" CD ARG C 35 " pdb=" NE ARG C 35 " pdb=" CZ ARG C 35 " ideal model delta sinusoidal sigma weight residual 180.00 -137.45 -42.55 2 1.50e+01 4.44e-03 9.76e+00 dihedral pdb=" N ARG C 19 " pdb=" CA ARG C 19 " pdb=" CB ARG C 19 " pdb=" CG ARG C 19 " ideal model delta sinusoidal sigma weight residual -180.00 -126.41 -53.59 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 3652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 667 0.042 - 0.084: 173 0.084 - 0.127: 63 0.127 - 0.169: 11 0.169 - 0.211: 3 Chirality restraints: 917 Sorted by residual: chirality pdb=" CA MET A 107 " pdb=" N MET A 107 " pdb=" C MET A 107 " pdb=" CB MET A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ARG C 36 " pdb=" N ARG C 36 " pdb=" C ARG C 36 " pdb=" CB ARG C 36 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE C 196 " pdb=" N ILE C 196 " pdb=" C ILE C 196 " pdb=" CB ILE C 196 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 914 not shown) Planarity restraints: 1087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 257 " 0.041 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO B 258 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 257 " 0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO C 258 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 258 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 258 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 16 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C GLU B 16 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU B 16 " -0.013 2.00e-02 2.50e+03 pdb=" N TRP B 17 " -0.011 2.00e-02 2.50e+03 ... (remaining 1084 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 377 2.74 - 3.28: 5390 3.28 - 3.82: 9209 3.82 - 4.36: 11042 4.36 - 4.90: 19448 Nonbonded interactions: 45466 Sorted by model distance: nonbonded pdb=" NH1 ARG B 170 " pdb=" OE2 GLU B 174 " model vdw 2.201 3.120 nonbonded pdb=" O THR C 84 " pdb=" OH TYR C 138 " model vdw 2.218 3.040 nonbonded pdb=" NH1 ARG A 170 " pdb=" OE2 GLU A 174 " model vdw 2.285 3.120 nonbonded pdb=" OE2 GLU B 167 " pdb=" NH2 ARG B 170 " model vdw 2.365 3.120 nonbonded pdb=" OE2 GLU A 22 " pdb=" NE2 GLN A 26 " model vdw 2.399 3.120 ... (remaining 45461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 44 or resid 83 through 279)) selection = (chain 'B' and (resid 9 through 44 or resid 83 through 279)) selection = (chain 'C' and resid 9 through 279) } 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: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.420 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.003 0.036 6118 Z= 0.174 Angle : 0.525 5.035 8294 Z= 0.318 Chirality : 0.045 0.211 917 Planarity : 0.004 0.062 1087 Dihedral : 13.530 88.754 2255 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.48 % Allowed : 0.96 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.26 (0.30), residues: 749 helix: 2.23 (0.33), residues: 247 sheet: -0.62 (0.38), residues: 184 loop : -0.97 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.010 0.001 HIS A 199 PHE 0.015 0.001 PHE C 178 TYR 0.006 0.001 TYR C 197 ARG 0.006 0.000 ARG B 223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 0.636 Fit side-chains REVERT: A 170 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7877 (ttp80) REVERT: B 171 LYS cc_start: 0.8289 (mtpp) cc_final: 0.7987 (mttt) REVERT: C 178 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6167 (m-80) outliers start: 3 outliers final: 1 residues processed: 125 average time/residue: 1.6919 time to fit residues: 218.4338 Evaluate side-chains 93 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 196 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 220 ASN C 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6118 Z= 0.131 Angle : 0.445 3.292 8294 Z= 0.240 Chirality : 0.043 0.135 917 Planarity : 0.004 0.050 1087 Dihedral : 4.206 52.230 850 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.93 % Allowed : 10.91 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.56 (0.30), residues: 749 helix: 2.45 (0.33), residues: 254 sheet: -0.31 (0.39), residues: 174 loop : -0.95 (0.29), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 96 HIS 0.007 0.001 HIS B 105 PHE 0.011 0.001 PHE C 92 TYR 0.017 0.001 TYR C 41 ARG 0.004 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.604 Fit side-chains REVERT: A 220 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7518 (m110) REVERT: A 238 ASP cc_start: 0.8626 (p0) cc_final: 0.8315 (p0) REVERT: B 171 LYS cc_start: 0.8252 (mtpp) cc_final: 0.8052 (mttt) REVERT: C 178 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6343 (m-80) REVERT: C 195 ARG cc_start: 0.7087 (mpt180) cc_final: 0.6867 (mmt180) outliers start: 12 outliers final: 5 residues processed: 96 average time/residue: 1.6015 time to fit residues: 159.2596 Evaluate side-chains 92 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 220 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS A 192 GLN B 163 GLN B 220 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6118 Z= 0.268 Angle : 0.552 4.415 8294 Z= 0.296 Chirality : 0.047 0.153 917 Planarity : 0.005 0.049 1087 Dihedral : 4.520 52.872 848 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.21 % Allowed : 11.08 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.35 (0.30), residues: 749 helix: 2.23 (0.33), residues: 252 sheet: -0.50 (0.38), residues: 176 loop : -0.95 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 96 HIS 0.011 0.002 HIS B 105 PHE 0.016 0.002 PHE C 130 TYR 0.019 0.002 TYR C 41 ARG 0.004 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.685 Fit side-chains REVERT: A 206 GLU cc_start: 0.6773 (tp30) cc_final: 0.6190 (tp30) REVERT: A 220 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7611 (m110) REVERT: B 171 LYS cc_start: 0.8308 (mtpp) cc_final: 0.8083 (mttt) REVERT: B 210 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7041 (mp10) REVERT: C 178 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.6516 (m-80) REVERT: C 195 ARG cc_start: 0.7112 (mpt180) cc_final: 0.6878 (mmt180) outliers start: 20 outliers final: 8 residues processed: 101 average time/residue: 1.5091 time to fit residues: 158.1367 Evaluate side-chains 101 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 60 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 163 GLN B 220 ASN C 220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6118 Z= 0.141 Angle : 0.446 3.409 8294 Z= 0.243 Chirality : 0.043 0.139 917 Planarity : 0.004 0.042 1087 Dihedral : 4.214 52.054 848 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.09 % Allowed : 13.16 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.51 (0.30), residues: 749 helix: 2.41 (0.32), residues: 253 sheet: -0.40 (0.39), residues: 175 loop : -0.93 (0.29), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.005 0.001 HIS B 105 PHE 0.011 0.002 PHE C 92 TYR 0.017 0.001 TYR C 41 ARG 0.003 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.700 Fit side-chains REVERT: A 206 GLU cc_start: 0.6750 (tp30) cc_final: 0.6136 (tp30) REVERT: A 238 ASP cc_start: 0.8703 (p0) cc_final: 0.8385 (p0) REVERT: B 171 LYS cc_start: 0.8288 (mtpp) cc_final: 0.8077 (mttt) REVERT: B 210 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7010 (mp10) REVERT: C 178 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6622 (m-80) REVERT: C 193 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7432 (mp) REVERT: C 195 ARG cc_start: 0.7101 (tpt170) cc_final: 0.6874 (mmt180) outliers start: 13 outliers final: 4 residues processed: 102 average time/residue: 1.5183 time to fit residues: 160.7947 Evaluate side-chains 100 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 196 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 192 GLN B 163 GLN B 220 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6118 Z= 0.185 Angle : 0.484 3.684 8294 Z= 0.261 Chirality : 0.044 0.145 917 Planarity : 0.004 0.044 1087 Dihedral : 4.292 50.641 848 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.89 % Allowed : 12.68 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 749 helix: 2.37 (0.32), residues: 253 sheet: -0.42 (0.39), residues: 174 loop : -0.95 (0.30), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.006 0.001 HIS A 199 PHE 0.013 0.002 PHE C 92 TYR 0.018 0.001 TYR C 41 ARG 0.005 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 0.634 Fit side-chains REVERT: A 206 GLU cc_start: 0.6744 (tp30) cc_final: 0.6148 (tp30) REVERT: B 171 LYS cc_start: 0.8287 (mtpp) cc_final: 0.8071 (mttt) REVERT: B 195 ARG cc_start: 0.7427 (mtt180) cc_final: 0.7070 (mtt-85) REVERT: B 210 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7043 (mp10) REVERT: C 195 ARG cc_start: 0.7142 (tpt170) cc_final: 0.6900 (mmt180) outliers start: 18 outliers final: 8 residues processed: 101 average time/residue: 1.6036 time to fit residues: 168.0939 Evaluate side-chains 101 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 163 GLN B 220 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6118 Z= 0.260 Angle : 0.546 4.556 8294 Z= 0.293 Chirality : 0.046 0.154 917 Planarity : 0.005 0.046 1087 Dihedral : 4.512 50.606 848 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.89 % Allowed : 13.16 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.28 (0.29), residues: 749 helix: 2.13 (0.32), residues: 252 sheet: -0.48 (0.38), residues: 174 loop : -1.00 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 96 HIS 0.007 0.001 HIS A 199 PHE 0.015 0.002 PHE C 130 TYR 0.019 0.002 TYR C 41 ARG 0.003 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.575 Fit side-chains REVERT: A 206 GLU cc_start: 0.6664 (tp30) cc_final: 0.6102 (tp30) REVERT: B 74 MET cc_start: 0.5588 (ptm) cc_final: 0.5328 (ptt) REVERT: B 171 LYS cc_start: 0.8317 (mtpp) cc_final: 0.8049 (mttt) REVERT: B 195 ARG cc_start: 0.7433 (mtt180) cc_final: 0.7073 (mtt-85) REVERT: B 210 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7021 (mp10) REVERT: C 195 ARG cc_start: 0.7190 (tpt170) cc_final: 0.6941 (mmt180) outliers start: 18 outliers final: 10 residues processed: 103 average time/residue: 1.5846 time to fit residues: 169.3397 Evaluate side-chains 100 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 0.0020 chunk 61 optimal weight: 0.0670 chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.4326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6118 Z= 0.122 Angle : 0.432 4.446 8294 Z= 0.235 Chirality : 0.042 0.137 917 Planarity : 0.004 0.038 1087 Dihedral : 4.099 49.416 848 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.57 % Allowed : 13.32 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.58 (0.30), residues: 749 helix: 2.54 (0.32), residues: 251 sheet: -0.37 (0.39), residues: 175 loop : -0.93 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 96 HIS 0.009 0.001 HIS A 199 PHE 0.010 0.001 PHE C 92 TYR 0.018 0.001 TYR C 41 ARG 0.004 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.624 Fit side-chains REVERT: A 135 ARG cc_start: 0.6612 (mtp-110) cc_final: 0.6296 (ttp80) REVERT: A 206 GLU cc_start: 0.6643 (tp30) cc_final: 0.6043 (tp30) REVERT: A 238 ASP cc_start: 0.8644 (p0) cc_final: 0.8302 (p0) REVERT: B 74 MET cc_start: 0.5475 (ptm) cc_final: 0.5271 (ptt) REVERT: B 171 LYS cc_start: 0.8247 (mtpp) cc_final: 0.8045 (mttt) REVERT: B 195 ARG cc_start: 0.7311 (mtt180) cc_final: 0.6917 (mtt-85) REVERT: B 210 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7045 (mp10) REVERT: C 103 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6619 (ptp-110) REVERT: C 195 ARG cc_start: 0.7169 (tpt170) cc_final: 0.6891 (mmt180) outliers start: 16 outliers final: 7 residues processed: 102 average time/residue: 1.4925 time to fit residues: 157.8737 Evaluate side-chains 99 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 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 192 GLN B 163 GLN B 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6118 Z= 0.167 Angle : 0.473 4.994 8294 Z= 0.254 Chirality : 0.043 0.143 917 Planarity : 0.004 0.041 1087 Dihedral : 4.196 49.103 848 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.05 % Allowed : 13.32 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.54 (0.30), residues: 749 helix: 2.48 (0.32), residues: 253 sheet: -0.37 (0.39), residues: 174 loop : -0.95 (0.30), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 96 HIS 0.007 0.001 HIS A 199 PHE 0.012 0.002 PHE C 92 TYR 0.019 0.001 TYR C 41 ARG 0.005 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.660 Fit side-chains REVERT: A 135 ARG cc_start: 0.6625 (mtp-110) cc_final: 0.6318 (ttp80) REVERT: A 206 GLU cc_start: 0.6675 (tp30) cc_final: 0.6089 (tp30) REVERT: B 195 ARG cc_start: 0.7325 (mtt180) cc_final: 0.6971 (mtt-85) REVERT: B 210 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7040 (mp10) REVERT: C 103 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6758 (ptp-110) REVERT: C 195 ARG cc_start: 0.7210 (tpt170) cc_final: 0.6928 (mmt180) outliers start: 19 outliers final: 9 residues processed: 101 average time/residue: 1.4438 time to fit residues: 151.4722 Evaluate side-chains 99 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 163 GLN B 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6118 Z= 0.158 Angle : 0.469 5.585 8294 Z= 0.252 Chirality : 0.043 0.142 917 Planarity : 0.004 0.041 1087 Dihedral : 4.172 48.650 848 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.73 % Allowed : 13.32 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.55 (0.30), residues: 749 helix: 2.51 (0.32), residues: 253 sheet: -0.38 (0.39), residues: 175 loop : -0.97 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 96 HIS 0.008 0.001 HIS A 199 PHE 0.012 0.002 PHE C 92 TYR 0.020 0.001 TYR C 41 ARG 0.005 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 0.671 Fit side-chains REVERT: A 135 ARG cc_start: 0.6608 (mtp-110) cc_final: 0.6266 (ttp80) REVERT: A 206 GLU cc_start: 0.6639 (tp30) cc_final: 0.6041 (tp30) REVERT: A 238 ASP cc_start: 0.8703 (p0) cc_final: 0.8382 (p0) REVERT: B 195 ARG cc_start: 0.7312 (mtt180) cc_final: 0.6914 (mtt-85) REVERT: B 210 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: C 103 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6695 (ptp-110) REVERT: C 195 ARG cc_start: 0.7206 (tpt170) cc_final: 0.6922 (mmt180) outliers start: 17 outliers final: 11 residues processed: 100 average time/residue: 1.4253 time to fit residues: 148.1023 Evaluate side-chains 102 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 0.0980 chunk 74 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN B 163 GLN B 220 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6118 Z= 0.153 Angle : 0.466 5.688 8294 Z= 0.250 Chirality : 0.043 0.141 917 Planarity : 0.004 0.041 1087 Dihedral : 4.141 48.177 848 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.25 % Allowed : 13.80 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.58 (0.30), residues: 749 helix: 2.53 (0.32), residues: 254 sheet: -0.37 (0.39), residues: 175 loop : -0.94 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 96 HIS 0.008 0.001 HIS A 199 PHE 0.012 0.002 PHE C 92 TYR 0.020 0.001 TYR C 41 ARG 0.005 0.000 ARG C 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.665 Fit side-chains REVERT: A 135 ARG cc_start: 0.6591 (mtp-110) cc_final: 0.6256 (ttp80) REVERT: A 206 GLU cc_start: 0.6639 (tp30) cc_final: 0.6040 (tp30) REVERT: A 238 ASP cc_start: 0.8689 (p0) cc_final: 0.8371 (p0) REVERT: B 195 ARG cc_start: 0.7321 (mtt180) cc_final: 0.6928 (mtt-85) REVERT: B 210 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7020 (mp10) REVERT: C 103 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6688 (ptp-110) REVERT: C 195 ARG cc_start: 0.7188 (tpt170) cc_final: 0.6900 (mmt180) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 1.5231 time to fit residues: 155.0170 Evaluate side-chains 101 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 0.0980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.155119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.123329 restraints weight = 6437.502| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.23 r_work: 0.3096 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6118 Z= 0.133 Angle : 0.446 5.823 8294 Z= 0.240 Chirality : 0.042 0.138 917 Planarity : 0.004 0.038 1087 Dihedral : 4.034 47.344 848 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.93 % Allowed : 14.29 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.75 % 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: 0.72 (0.30), residues: 749 helix: 2.72 (0.32), residues: 251 sheet: -0.31 (0.39), residues: 175 loop : -0.88 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.007 0.001 HIS A 199 PHE 0.011 0.001 PHE C 92 TYR 0.022 0.001 TYR C 41 ARG 0.005 0.000 ARG C 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3225.58 seconds wall clock time: 60 minutes 49.06 seconds (3649.06 seconds total)