Starting phenix.real_space_refine on Fri Jul 19 02:44:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4q_42975/07_2024/8v4q_42975.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4q_42975/07_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_42975/07_2024/8v4q_42975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4q_42975/07_2024/8v4q_42975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4q_42975/07_2024/8v4q_42975.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v4q_42975/07_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-5388/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: 4.41, per 1000 atoms: 0.74 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 1.1 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: 0.71 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: 1.64 Time building geometry restraints manager: 2.20 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 2.520 nonbonded pdb=" O THR C 84 " pdb=" OH TYR C 138 " model vdw 2.218 2.440 nonbonded pdb=" NH1 ARG A 170 " pdb=" OE2 GLU A 174 " model vdw 2.285 2.520 nonbonded pdb=" OE2 GLU B 167 " pdb=" NH2 ARG B 170 " model vdw 2.365 2.520 nonbonded pdb=" OE2 GLU A 22 " pdb=" NE2 GLN A 26 " model vdw 2.399 2.520 ... (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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.270 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.050 ------------------------------------------------------------------------------- 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 : 0.728 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: 1.6662 time to fit residues: 215.1343 Evaluate side-chains 93 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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** C 220 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6118 Z= 0.266 Angle : 0.556 4.702 8294 Z= 0.297 Chirality : 0.047 0.151 917 Planarity : 0.005 0.051 1087 Dihedral : 4.738 53.542 850 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.37 % Allowed : 9.79 % Favored : 86.84 % 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: 0.25 (0.30), residues: 749 helix: 2.12 (0.33), residues: 252 sheet: -0.55 (0.38), residues: 176 loop : -0.99 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.014 0.002 HIS B 105 PHE 0.016 0.002 PHE C 130 TYR 0.018 0.002 TYR C 41 ARG 0.004 0.000 ARG A 29 *********************** 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 114 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.729 Fit side-chains REVERT: A 220 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7612 (m110) REVERT: B 171 LYS cc_start: 0.8330 (mtpp) cc_final: 0.8050 (mttt) REVERT: C 178 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6386 (m-80) REVERT: C 195 ARG cc_start: 0.7121 (mpt180) cc_final: 0.6909 (mmt180) outliers start: 21 outliers final: 9 residues processed: 99 average time/residue: 1.5761 time to fit residues: 162.1445 Evaluate side-chains 103 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 220 ASN Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 169 THR 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 226 SER Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6118 Z= 0.224 Angle : 0.515 4.337 8294 Z= 0.277 Chirality : 0.045 0.148 917 Planarity : 0.005 0.047 1087 Dihedral : 4.525 53.291 848 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.05 % Allowed : 11.88 % Favored : 85.07 % 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: 0.27 (0.29), residues: 749 helix: 2.13 (0.32), residues: 252 sheet: -0.54 (0.38), residues: 176 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 B 105 PHE 0.013 0.002 PHE C 92 TYR 0.017 0.001 TYR C 41 ARG 0.003 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: 19 poor density : 95 time to evaluate : 0.686 Fit side-chains REVERT: A 220 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7616 (m110) REVERT: B 171 LYS cc_start: 0.8346 (mtpp) cc_final: 0.8047 (mttt) REVERT: B 210 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7035 (mp10) REVERT: C 178 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6483 (m-80) REVERT: C 195 ARG cc_start: 0.7185 (mpt180) cc_final: 0.6959 (mmt180) outliers start: 19 outliers final: 10 residues processed: 101 average time/residue: 1.5843 time to fit residues: 166.3360 Evaluate side-chains 104 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 226 SER 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: 8.9990 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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: 0.8448 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6118 Z= 0.396 Angle : 0.643 5.769 8294 Z= 0.344 Chirality : 0.051 0.188 917 Planarity : 0.006 0.048 1087 Dihedral : 4.940 54.875 848 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.17 % Allowed : 12.20 % 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: -0.07 (0.29), residues: 749 helix: 1.66 (0.32), residues: 252 sheet: -0.62 (0.38), residues: 174 loop : -1.07 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 96 HIS 0.009 0.002 HIS B 105 PHE 0.020 0.003 PHE C 130 TYR 0.011 0.002 TYR B 131 ARG 0.005 0.001 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 114 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 0.684 Fit side-chains REVERT: A 220 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7713 (m110) REVERT: B 74 MET cc_start: 0.5715 (OUTLIER) cc_final: 0.5494 (ptt) REVERT: B 171 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8136 (mttt) REVERT: B 210 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7143 (mp10) REVERT: C 178 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6584 (m-80) REVERT: C 195 ARG cc_start: 0.7221 (mpt180) cc_final: 0.6954 (mmt180) outliers start: 26 outliers final: 12 residues processed: 102 average time/residue: 1.4167 time to fit residues: 150.2791 Evaluate side-chains 103 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 16 GLU 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 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6118 Z= 0.172 Angle : 0.479 4.737 8294 Z= 0.259 Chirality : 0.044 0.143 917 Planarity : 0.004 0.040 1087 Dihedral : 4.471 53.925 848 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.53 % Allowed : 13.96 % Favored : 82.50 % 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 (0.29), residues: 749 helix: 2.10 (0.32), residues: 252 sheet: -0.48 (0.39), residues: 174 loop : -1.00 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 96 HIS 0.005 0.001 HIS B 201 PHE 0.012 0.002 PHE C 92 TYR 0.010 0.001 TYR C 89 ARG 0.003 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: 22 poor density : 89 time to evaluate : 0.702 Fit side-chains REVERT: A 220 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7679 (m110) REVERT: B 171 LYS cc_start: 0.8315 (mtpp) cc_final: 0.8037 (mttt) REVERT: B 210 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7035 (mp10) REVERT: C 178 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: C 195 ARG cc_start: 0.7197 (mpt180) cc_final: 0.6934 (mmt180) outliers start: 22 outliers final: 10 residues processed: 103 average time/residue: 1.4772 time to fit residues: 157.9975 Evaluate side-chains 101 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 51 VAL 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 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 226 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.0170 chunk 72 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 overall best weight: 1.1622 ------------------------------------------------------------------------------- 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6118 Z= 0.209 Angle : 0.507 4.223 8294 Z= 0.273 Chirality : 0.045 0.149 917 Planarity : 0.004 0.043 1087 Dihedral : 4.498 54.219 848 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.69 % Allowed : 14.45 % Favored : 81.86 % 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: 0.30 (0.30), residues: 749 helix: 2.17 (0.32), residues: 253 sheet: -0.50 (0.38), residues: 174 loop : -0.99 (0.30), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 96 HIS 0.004 0.001 HIS B 7 PHE 0.013 0.002 PHE C 92 TYR 0.010 0.001 TYR C 89 ARG 0.005 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 112 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 0.728 Fit side-chains REVERT: A 220 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7710 (m110) REVERT: B 171 LYS cc_start: 0.8320 (mtpp) cc_final: 0.8055 (mttt) REVERT: B 210 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7033 (mp10) REVERT: C 195 ARG cc_start: 0.7220 (mpt180) cc_final: 0.6953 (mmt180) outliers start: 23 outliers final: 12 residues processed: 101 average time/residue: 1.4437 time to fit residues: 151.6127 Evaluate side-chains 102 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 51 VAL 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 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 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 226 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 52 optimal weight: 0.0370 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 43 optimal weight: 0.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6118 Z= 0.165 Angle : 0.474 4.458 8294 Z= 0.255 Chirality : 0.043 0.141 917 Planarity : 0.004 0.040 1087 Dihedral : 4.356 53.678 848 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.53 % Allowed : 14.61 % Favored : 81.86 % 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: 0.43 (0.30), residues: 749 helix: 2.36 (0.32), residues: 253 sheet: -0.46 (0.39), residues: 175 loop : -0.98 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 96 HIS 0.003 0.001 HIS B 7 PHE 0.012 0.002 PHE C 92 TYR 0.012 0.001 TYR C 89 ARG 0.005 0.000 ARG C 29 *********************** 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 115 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 0.698 Fit side-chains REVERT: A 220 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.7693 (m110) REVERT: B 171 LYS cc_start: 0.8287 (mtpp) cc_final: 0.8040 (mttt) REVERT: C 195 ARG cc_start: 0.7219 (mpt180) cc_final: 0.6949 (mmt180) outliers start: 22 outliers final: 12 residues processed: 105 average time/residue: 1.4299 time to fit residues: 156.0772 Evaluate side-chains 105 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL 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 51 VAL Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 169 THR 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 226 SER Chi-restraints excluded: chain C residue 253 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 0.0870 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 0.0970 overall best weight: 1.0362 ------------------------------------------------------------------------------- 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: 0.8389 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6118 Z= 0.191 Angle : 0.496 4.207 8294 Z= 0.266 Chirality : 0.044 0.145 917 Planarity : 0.004 0.041 1087 Dihedral : 4.408 53.818 848 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.37 % Allowed : 14.93 % Favored : 81.70 % 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: 0.39 (0.30), residues: 749 helix: 2.30 (0.32), residues: 253 sheet: -0.48 (0.38), residues: 175 loop : -0.97 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 96 HIS 0.004 0.001 HIS B 7 PHE 0.013 0.002 PHE C 92 TYR 0.011 0.001 TYR C 89 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 113 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.696 Fit side-chains REVERT: A 220 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7710 (m110) REVERT: B 171 LYS cc_start: 0.8293 (mtpp) cc_final: 0.8048 (mttt) REVERT: B 210 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7048 (mp10) REVERT: C 195 ARG cc_start: 0.7236 (mpt180) cc_final: 0.6963 (mmt180) outliers start: 21 outliers final: 12 residues processed: 103 average time/residue: 1.4522 time to fit residues: 155.4582 Evaluate side-chains 106 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL 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 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 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 226 SER 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: 3.9990 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 0.0050 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.7398 ------------------------------------------------------------------------------- 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 ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6118 Z= 0.286 Angle : 0.570 4.578 8294 Z= 0.305 Chirality : 0.047 0.157 917 Planarity : 0.005 0.044 1087 Dihedral : 4.672 54.392 848 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.89 % Allowed : 16.21 % Favored : 80.90 % 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: 0.20 (0.29), residues: 749 helix: 2.02 (0.32), residues: 252 sheet: -0.53 (0.38), residues: 174 loop : -0.99 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 96 HIS 0.006 0.001 HIS B 7 PHE 0.017 0.002 PHE C 130 TYR 0.012 0.002 TYR C 89 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 108 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.730 Fit side-chains REVERT: A 220 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7738 (m110) REVERT: B 171 LYS cc_start: 0.8327 (mtpp) cc_final: 0.8085 (mttt) REVERT: B 210 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7111 (mp10) outliers start: 18 outliers final: 12 residues processed: 99 average time/residue: 1.4537 time to fit residues: 149.5905 Evaluate side-chains 102 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL 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 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 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 226 SER 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: 2.9990 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1706 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= 0.146 Angle : 0.462 5.006 8294 Z= 0.249 Chirality : 0.043 0.138 917 Planarity : 0.004 0.037 1087 Dihedral : 4.318 53.965 848 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.57 % Allowed : 16.21 % Favored : 81.22 % 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: 0.47 (0.30), residues: 749 helix: 2.39 (0.32), residues: 253 sheet: -0.43 (0.39), residues: 175 loop : -0.95 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 96 HIS 0.007 0.001 HIS B 201 PHE 0.011 0.001 PHE C 92 TYR 0.013 0.001 TYR C 89 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 110 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.649 Fit side-chains REVERT: A 135 ARG cc_start: 0.6714 (mtp-110) cc_final: 0.6390 (ttp80) REVERT: A 238 ASP cc_start: 0.8705 (p0) cc_final: 0.8390 (p0) REVERT: B 171 LYS cc_start: 0.8240 (mtpp) cc_final: 0.8015 (mttt) REVERT: B 210 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7022 (mp10) outliers start: 16 outliers final: 12 residues processed: 101 average time/residue: 1.4418 time to fit residues: 151.3455 Evaluate side-chains 105 residues out of total 623 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 244 ASP 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 178 PHE Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 226 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.9980 chunk 8 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.161190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.131909 restraints weight = 6843.470| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.00 r_work: 0.3286 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1699 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= 0.149 Angle : 0.458 4.489 8294 Z= 0.246 Chirality : 0.043 0.139 917 Planarity : 0.004 0.038 1087 Dihedral : 4.235 53.985 848 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.41 % Allowed : 16.69 % Favored : 80.90 % 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: 0.61 (0.30), residues: 749 helix: 2.54 (0.32), residues: 253 sheet: -0.36 (0.39), residues: 175 loop : -0.90 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 96 HIS 0.003 0.001 HIS B 199 PHE 0.012 0.002 PHE C 92 TYR 0.012 0.001 TYR C 89 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: 3169.99 seconds wall clock time: 55 minutes 34.69 seconds (3334.69 seconds total)