Starting phenix.real_space_refine on Tue Feb 13 08:42:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0t_26950/02_2024/7v0t_26950.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0t_26950/02_2024/7v0t_26950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0t_26950/02_2024/7v0t_26950.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0t_26950/02_2024/7v0t_26950.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0t_26950/02_2024/7v0t_26950.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0t_26950/02_2024/7v0t_26950.pdb" } resolution = 2.7 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= 0.001 sd= 0.277 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 12 5.16 5 C 2941 2.51 5 N 805 2.21 5 O 900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 60": "OE1" <-> "OE2" Residue "E PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 125": "OE1" <-> "OE2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "E GLU 252": "OE1" <-> "OE2" Residue "E ASP 277": "OD1" <-> "OD2" Residue "E TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E GLU 312": "OE1" <-> "OE2" Residue "E PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 45": "OD1" <-> "OD2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C ASP 143": "OD1" <-> "OD2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 325": "OD1" <-> "OD2" Residue "C GLU 341": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4658 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2276 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2343 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Time building chain proxies: 2.93, per 1000 atoms: 0.63 Number of scatterers: 4658 At special positions: 0 Unit cell: (89.225, 82.585, 75.53, 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 12 16.00 O 900 8.00 N 805 7.00 C 2941 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: 1.89 Conformation dependent library (CDL) restraints added in 840.4 milliseconds 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1108 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 3 sheets defined 41.3% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.817A pdb=" N LYS E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 142 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'E' and resid 194 through 201 Processing helix chain 'E' and resid 277 through 291 Processing helix chain 'E' and resid 291 through 300 Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.738A pdb=" N LEU E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 334 Processing helix chain 'E' and resid 335 through 349 removed outlier: 4.147A pdb=" N SER E 349 " --> pdb=" O ARG E 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 103 through 116 removed outlier: 3.842A pdb=" N LYS C 116 " --> pdb=" O ARG C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 163 through 170 removed outlier: 3.588A pdb=" N LEU C 167 " --> pdb=" O HIS C 163 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 201 Processing helix chain 'C' and resid 277 through 291 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 303 through 317 removed outlier: 3.696A pdb=" N LEU C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 334 Processing helix chain 'C' and resid 334 through 343 removed outlier: 4.139A pdb=" N VAL C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 59 through 67 removed outlier: 6.493A pdb=" N VAL E 59 " --> pdb=" O ARG E 80 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG E 80 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU E 61 " --> pdb=" O ALA E 78 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 85 through 87 current: chain 'E' and resid 184 through 185 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 184 through 185 current: chain 'E' and resid 262 through 270 Processing sheet with id=AA2, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AA3, first strand: chain 'C' and resid 56 through 66 removed outlier: 6.556A pdb=" N VAL C 59 " --> pdb=" O ARG C 80 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG C 80 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU C 61 " --> pdb=" O ALA C 78 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 85 through 87 current: chain 'C' and resid 224 through 234 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 224 through 234 current: chain 'C' and resid 262 through 270 164 hydrogen bonds defined for protein. 468 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: 1.06 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1574 1.34 - 1.46: 884 1.46 - 1.58: 2235 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 4713 Sorted by residual: bond pdb=" N PRO C 221 " pdb=" CA PRO C 221 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.31e-02 5.83e+03 1.61e+00 bond pdb=" CB GLN E 124 " pdb=" CG GLN E 124 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" CG1 ILE C 140 " pdb=" CD1 ILE C 140 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.15e+00 bond pdb=" CA ILE C 216 " pdb=" CB ILE C 216 " ideal model delta sigma weight residual 1.540 1.568 -0.028 2.70e-02 1.37e+03 1.08e+00 bond pdb=" CG GLN E 124 " pdb=" CD GLN E 124 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.07e+00 ... (remaining 4708 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.50: 159 106.50 - 113.39: 2598 113.39 - 120.28: 1634 120.28 - 127.17: 1953 127.17 - 134.06: 61 Bond angle restraints: 6405 Sorted by residual: angle pdb=" N ASN C 91 " pdb=" CA ASN C 91 " pdb=" C ASN C 91 " ideal model delta sigma weight residual 114.09 109.26 4.83 1.55e+00 4.16e-01 9.69e+00 angle pdb=" CB GLN E 124 " pdb=" CG GLN E 124 " pdb=" CD GLN E 124 " ideal model delta sigma weight residual 112.60 117.66 -5.06 1.70e+00 3.46e-01 8.86e+00 angle pdb=" C LEU C 335 " pdb=" N VAL C 336 " pdb=" CA VAL C 336 " ideal model delta sigma weight residual 120.33 122.60 -2.27 8.00e-01 1.56e+00 8.06e+00 angle pdb=" CA GLN E 124 " pdb=" CB GLN E 124 " pdb=" CG GLN E 124 " ideal model delta sigma weight residual 114.10 119.52 -5.42 2.00e+00 2.50e-01 7.34e+00 angle pdb=" CA PRO C 271 " pdb=" C PRO C 271 " pdb=" N GLU C 272 " ideal model delta sigma weight residual 114.74 117.11 -2.37 1.03e+00 9.43e-01 5.30e+00 ... (remaining 6400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2432 17.95 - 35.90: 294 35.90 - 53.86: 99 53.86 - 71.81: 29 71.81 - 89.76: 17 Dihedral angle restraints: 2871 sinusoidal: 1175 harmonic: 1696 Sorted by residual: dihedral pdb=" CA TRP E 81 " pdb=" C TRP E 81 " pdb=" N VAL E 82 " pdb=" CA VAL E 82 " ideal model delta harmonic sigma weight residual 180.00 157.25 22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CG ARG C 246 " pdb=" CD ARG C 246 " pdb=" NE ARG C 246 " pdb=" CZ ARG C 246 " ideal model delta sinusoidal sigma weight residual -90.00 -134.83 44.83 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU C 32 " pdb=" CG GLU C 32 " pdb=" CD GLU C 32 " pdb=" OE1 GLU C 32 " ideal model delta sinusoidal sigma weight residual 0.00 88.72 -88.72 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 2868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 567 0.045 - 0.090: 123 0.090 - 0.135: 38 0.135 - 0.180: 4 0.180 - 0.225: 1 Chirality restraints: 733 Sorted by residual: chirality pdb=" CB ILE C 216 " pdb=" CA ILE C 216 " pdb=" CG1 ILE C 216 " pdb=" CG2 ILE C 216 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE E 276 " pdb=" CA ILE E 276 " pdb=" CG1 ILE E 276 " pdb=" CG2 ILE E 276 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CA VAL E 82 " pdb=" N VAL E 82 " pdb=" C VAL E 82 " pdb=" CB VAL E 82 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 730 not shown) Planarity restraints: 840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 273 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO E 274 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 274 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 274 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 326 " 0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO C 327 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 327 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 327 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 146 " -0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO C 147 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 147 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 147 " -0.018 5.00e-02 4.00e+02 ... (remaining 837 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 138 2.70 - 3.25: 4322 3.25 - 3.80: 7907 3.80 - 4.35: 10331 4.35 - 4.90: 16454 Nonbonded interactions: 39152 Sorted by model distance: nonbonded pdb=" OG1 THR E 179 " pdb=" O ASP E 183 " model vdw 2.151 2.440 nonbonded pdb=" NE2 HIS E 275 " pdb=" OE1 GLU C 312 " model vdw 2.195 2.520 nonbonded pdb=" NH1 ARG C 233 " pdb=" O HOH C1001 " model vdw 2.271 2.520 nonbonded pdb=" O TYR C 46 " pdb=" O HOH C1002 " model vdw 2.276 2.440 nonbonded pdb=" OE1 GLU C 225 " pdb=" OH TYR C 299 " model vdw 2.293 2.440 ... (remaining 39147 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 'C' and (resid 56 through 203 or resid 217 through 348)) selection = (chain 'E' and ((resid 56 and (name N or name CA or name C or name O or name CB \ )) or resid 57 through 181 or resid 192 through 348)) } 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: 0.790 Set stop_for_unknowns flag: 0.010 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: 4.070 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.370 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.004 0.042 4713 Z= 0.246 Angle : 0.631 7.174 6405 Z= 0.333 Chirality : 0.042 0.225 733 Planarity : 0.005 0.036 840 Dihedral : 19.430 89.760 1763 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.57 % Favored : 98.26 % Rotamer: Outliers : 3.45 % Allowed : 27.79 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.33), residues: 574 helix: 0.62 (0.34), residues: 219 sheet: 1.76 (0.57), residues: 84 loop : -0.18 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 81 HIS 0.003 0.001 HIS E 163 PHE 0.022 0.002 PHE C 314 TYR 0.019 0.002 TYR E 278 ARG 0.004 0.001 ARG E 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 0.528 Fit side-chains REVERT: C 83 GLN cc_start: 0.7179 (mt0) cc_final: 0.6971 (mp10) REVERT: C 109 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8112 (mp0) outliers start: 17 outliers final: 12 residues processed: 84 average time/residue: 1.3726 time to fit residues: 119.4008 Evaluate side-chains 82 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 265 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 23 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 GLN E 275 HIS ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.0543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4713 Z= 0.174 Angle : 0.504 6.732 6405 Z= 0.248 Chirality : 0.038 0.157 733 Planarity : 0.004 0.029 840 Dihedral : 6.967 56.430 648 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.74 % Favored : 98.08 % Rotamer: Outliers : 4.67 % Allowed : 25.56 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.34), residues: 574 helix: 1.17 (0.35), residues: 220 sheet: 1.99 (0.58), residues: 84 loop : -0.04 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 81 HIS 0.002 0.001 HIS E 309 PHE 0.019 0.002 PHE C 314 TYR 0.011 0.001 TYR E 278 ARG 0.003 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 70 time to evaluate : 0.472 Fit side-chains REVERT: C 114 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7980 (m-80) outliers start: 23 outliers final: 12 residues processed: 85 average time/residue: 1.4136 time to fit residues: 124.1271 Evaluate side-chains 83 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 46 optimal weight: 0.0770 chunk 17 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.2980 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 HIS C 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4713 Z= 0.162 Angle : 0.478 6.955 6405 Z= 0.237 Chirality : 0.038 0.151 733 Planarity : 0.003 0.029 840 Dihedral : 6.433 59.042 641 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.39 % Favored : 98.43 % Rotamer: Outliers : 4.46 % Allowed : 26.77 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.35), residues: 574 helix: 1.44 (0.36), residues: 220 sheet: 1.76 (0.57), residues: 88 loop : 0.05 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 81 HIS 0.002 0.001 HIS E 309 PHE 0.019 0.002 PHE C 314 TYR 0.011 0.001 TYR E 278 ARG 0.002 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 68 time to evaluate : 0.561 Fit side-chains REVERT: E 149 ASP cc_start: 0.6613 (OUTLIER) cc_final: 0.5964 (m-30) REVERT: E 291 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: C 114 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7905 (m-80) outliers start: 22 outliers final: 11 residues processed: 82 average time/residue: 1.4243 time to fit residues: 120.6421 Evaluate side-chains 84 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 70 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 275 HIS C 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4713 Z= 0.179 Angle : 0.492 7.061 6405 Z= 0.240 Chirality : 0.038 0.149 733 Planarity : 0.003 0.029 840 Dihedral : 6.070 58.982 638 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.74 % Favored : 98.08 % Rotamer: Outliers : 5.07 % Allowed : 25.96 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.35), residues: 574 helix: 1.43 (0.36), residues: 220 sheet: 1.75 (0.56), residues: 88 loop : 0.07 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 81 HIS 0.002 0.001 HIS E 309 PHE 0.019 0.002 PHE C 314 TYR 0.011 0.001 TYR E 278 ARG 0.003 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 0.524 Fit side-chains REVERT: E 116 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7512 (ptmm) REVERT: E 125 GLU cc_start: 0.6222 (mm-30) cc_final: 0.6010 (mm-30) REVERT: E 149 ASP cc_start: 0.6619 (OUTLIER) cc_final: 0.5960 (m-30) REVERT: E 291 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: C 109 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: C 114 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: C 272 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7433 (mp0) outliers start: 25 outliers final: 14 residues processed: 92 average time/residue: 1.4589 time to fit residues: 138.4880 Evaluate side-chains 92 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 338 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 239 GLN E 275 HIS C 148 GLN C 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 4713 Z= 0.384 Angle : 0.622 9.105 6405 Z= 0.308 Chirality : 0.044 0.150 733 Planarity : 0.005 0.032 840 Dihedral : 6.501 59.349 638 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 6.09 % Allowed : 24.95 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.34), residues: 574 helix: 1.00 (0.35), residues: 220 sheet: 2.08 (0.58), residues: 78 loop : -0.27 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 81 HIS 0.004 0.001 HIS C 275 PHE 0.026 0.003 PHE C 314 TYR 0.017 0.002 TYR C 278 ARG 0.003 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 75 time to evaluate : 0.477 Fit side-chains REVERT: E 116 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7608 (ptmm) REVERT: E 149 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.6080 (m-30) REVERT: E 159 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8086 (mp) REVERT: E 166 GLU cc_start: 0.6960 (pm20) cc_final: 0.6570 (pm20) REVERT: E 291 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: C 114 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: C 272 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7518 (mp0) outliers start: 30 outliers final: 14 residues processed: 92 average time/residue: 1.3855 time to fit residues: 131.7783 Evaluate side-chains 94 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 338 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 28 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 239 GLN E 275 HIS C 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4713 Z= 0.198 Angle : 0.512 8.206 6405 Z= 0.250 Chirality : 0.039 0.150 733 Planarity : 0.003 0.029 840 Dihedral : 6.136 56.376 638 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.87 % Allowed : 26.77 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.34), residues: 574 helix: 1.26 (0.36), residues: 219 sheet: 1.55 (0.55), residues: 88 loop : -0.10 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 81 HIS 0.002 0.001 HIS E 309 PHE 0.021 0.002 PHE C 314 TYR 0.011 0.002 TYR C 278 ARG 0.002 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 0.545 Fit side-chains REVERT: E 149 ASP cc_start: 0.6665 (OUTLIER) cc_final: 0.6017 (m-30) REVERT: E 166 GLU cc_start: 0.6950 (pm20) cc_final: 0.6628 (pm20) REVERT: E 291 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8028 (tm-30) REVERT: C 114 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: C 272 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7484 (mp0) outliers start: 24 outliers final: 12 residues processed: 90 average time/residue: 1.5481 time to fit residues: 143.6351 Evaluate side-chains 91 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 272 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 30 optimal weight: 0.4980 chunk 54 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 239 GLN E 275 HIS C 148 GLN C 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4713 Z= 0.380 Angle : 0.624 9.245 6405 Z= 0.310 Chirality : 0.044 0.151 733 Planarity : 0.005 0.037 840 Dihedral : 6.441 59.393 638 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 6.09 % Allowed : 24.75 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.34), residues: 574 helix: 0.93 (0.35), residues: 220 sheet: 1.99 (0.58), residues: 78 loop : -0.34 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 81 HIS 0.003 0.001 HIS E 309 PHE 0.026 0.003 PHE C 314 TYR 0.016 0.002 TYR C 278 ARG 0.003 0.001 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 75 time to evaluate : 0.527 Fit side-chains REVERT: E 149 ASP cc_start: 0.6751 (OUTLIER) cc_final: 0.6142 (m-30) REVERT: E 291 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: C 114 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.7637 (m-80) REVERT: C 272 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7525 (mp0) outliers start: 30 outliers final: 15 residues processed: 93 average time/residue: 1.3464 time to fit residues: 129.5745 Evaluate side-chains 91 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 338 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 chunk 30 optimal weight: 0.0270 overall best weight: 0.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 239 GLN E 275 HIS C 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4713 Z= 0.134 Angle : 0.488 7.467 6405 Z= 0.237 Chirality : 0.038 0.150 733 Planarity : 0.003 0.031 840 Dihedral : 5.905 55.075 638 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.67 % Allowed : 26.37 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.34), residues: 574 helix: 1.45 (0.36), residues: 219 sheet: 1.52 (0.55), residues: 88 loop : -0.01 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 81 HIS 0.002 0.000 HIS E 309 PHE 0.018 0.002 PHE C 314 TYR 0.006 0.001 TYR C 278 ARG 0.002 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.516 Fit side-chains REVERT: E 149 ASP cc_start: 0.6667 (OUTLIER) cc_final: 0.6036 (m-30) REVERT: E 291 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.8001 (tm-30) REVERT: C 114 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: C 272 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7489 (mp0) outliers start: 23 outliers final: 13 residues processed: 93 average time/residue: 1.4481 time to fit residues: 139.0174 Evaluate side-chains 91 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 272 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 48 optimal weight: 0.0020 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 239 GLN E 275 HIS C 148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4713 Z= 0.141 Angle : 0.473 6.475 6405 Z= 0.231 Chirality : 0.037 0.147 733 Planarity : 0.003 0.033 840 Dihedral : 5.137 53.653 635 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.85 % Allowed : 26.37 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.35), residues: 574 helix: 1.68 (0.37), residues: 220 sheet: 1.55 (0.55), residues: 88 loop : 0.07 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 81 HIS 0.001 0.000 HIS E 309 PHE 0.017 0.001 PHE C 314 TYR 0.008 0.001 TYR C 278 ARG 0.006 0.000 ARG C 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.548 Fit side-chains REVERT: E 112 ARG cc_start: 0.7944 (ttm110) cc_final: 0.7439 (ttm110) REVERT: E 149 ASP cc_start: 0.6663 (OUTLIER) cc_final: 0.6052 (m-30) REVERT: C 112 ARG cc_start: 0.8000 (ttp-110) cc_final: 0.7779 (ttm-80) REVERT: C 114 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: C 300 MET cc_start: 0.8133 (mtt) cc_final: 0.7915 (mtp) outliers start: 19 outliers final: 10 residues processed: 88 average time/residue: 1.4612 time to fit residues: 132.8415 Evaluate side-chains 86 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 13 optimal weight: 0.2980 chunk 41 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 239 GLN E 275 HIS C 148 GLN C 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4713 Z= 0.212 Angle : 0.530 7.626 6405 Z= 0.254 Chirality : 0.039 0.146 733 Planarity : 0.004 0.030 840 Dihedral : 5.255 56.610 635 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.65 % Allowed : 27.18 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.34), residues: 574 helix: 1.57 (0.36), residues: 220 sheet: 1.56 (0.55), residues: 88 loop : 0.06 (0.36), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 81 HIS 0.003 0.001 HIS E 309 PHE 0.020 0.002 PHE C 314 TYR 0.012 0.002 TYR C 278 ARG 0.004 0.000 ARG C 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1148 Ramachandran restraints generated. 574 Oldfield, 0 Emsley, 574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 0.529 Fit side-chains REVERT: E 112 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7464 (ttm110) REVERT: E 149 ASP cc_start: 0.6665 (OUTLIER) cc_final: 0.6076 (m-30) REVERT: C 112 ARG cc_start: 0.8021 (ttp-110) cc_final: 0.7790 (ttm-80) REVERT: C 114 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: C 272 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7502 (mp0) outliers start: 18 outliers final: 11 residues processed: 86 average time/residue: 1.5688 time to fit residues: 139.0686 Evaluate side-chains 89 residues out of total 505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 223 ASP Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 272 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 239 GLN E 275 HIS C 148 GLN C 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.173210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.130524 restraints weight = 4510.750| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.34 r_work: 0.3061 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 4713 Z= 0.426 Angle : 0.677 9.397 6405 Z= 0.330 Chirality : 0.045 0.148 733 Planarity : 0.005 0.038 840 Dihedral : 5.717 56.999 635 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.26 % Allowed : 26.77 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.33), residues: 574 helix: 1.00 (0.35), residues: 220 sheet: 1.91 (0.57), residues: 78 loop : -0.30 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 81 HIS 0.004 0.001 HIS E 309 PHE 0.026 0.003 PHE C 314 TYR 0.016 0.002 TYR C 278 ARG 0.004 0.001 ARG C 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2808.04 seconds wall clock time: 49 minutes 52.66 seconds (2992.66 seconds total)