Starting phenix.real_space_refine on Fri Apr 5 21:57:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7til_25913/04_2024/7til_25913.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7til_25913/04_2024/7til_25913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7til_25913/04_2024/7til_25913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7til_25913/04_2024/7til_25913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7til_25913/04_2024/7til_25913.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7til_25913/04_2024/7til_25913.pdb" } resolution = 3.7 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= -0.000 sd= 0.005 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 3707 2.51 5 N 1037 2.21 5 O 1059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 337": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5815 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2876 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 341} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2939 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 349} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 3.60, per 1000 atoms: 0.62 Number of scatterers: 5815 At special positions: 0 Unit cell: (65.65, 107.25, 112.45, 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 1059 8.00 N 1037 7.00 C 3707 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: 2.04 Conformation dependent library (CDL) restraints added in 849.0 milliseconds 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 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: 43 helices and 4 sheets defined 55.6% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 removed outlier: 3.616A pdb=" N GLN A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 26 Processing helix chain 'A' and resid 27 through 31 removed outlier: 3.847A pdb=" N TRP A 31 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 48 Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.676A pdb=" N VAL A 52 " --> pdb=" O ASN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 100 Processing helix chain 'A' and resid 101 through 118 removed outlier: 3.516A pdb=" N GLN A 117 " --> pdb=" O TYR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 129 through 136 removed outlier: 4.328A pdb=" N TRP A 133 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N THR A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 150 Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.625A pdb=" N ALA A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 189 removed outlier: 3.561A pdb=" N ARG A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 removed outlier: 3.994A pdb=" N GLU A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 273 through 277 removed outlier: 3.639A pdb=" N ALA A 277 " --> pdb=" O HIS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 307 Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.970A pdb=" N VAL A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 367 removed outlier: 3.593A pdb=" N TYR A 366 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.626A pdb=" N VAL A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 16 removed outlier: 3.582A pdb=" N GLN B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 26 Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 48 through 61 removed outlier: 4.028A pdb=" N VAL B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 100 removed outlier: 3.615A pdb=" N ASP B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 118 removed outlier: 3.552A pdb=" N GLU B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 129 through 135 removed outlier: 4.273A pdb=" N TRP B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 150 removed outlier: 3.567A pdb=" N GLN B 150 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.727A pdb=" N LEU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 160 through 165' Processing helix chain 'B' and resid 177 through 189 removed outlier: 3.567A pdb=" N GLU B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 197 removed outlier: 3.828A pdb=" N GLU B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 293 through 307 Processing helix chain 'B' and resid 316 through 323 removed outlier: 3.551A pdb=" N PHE B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.565A pdb=" N VAL B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 381 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 removed outlier: 3.578A pdb=" N GLN A 33 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 89 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 66 " --> pdb=" O HIS A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 230 removed outlier: 3.595A pdb=" N VAL A 214 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 244 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N TRP A 289 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A 246 " --> pdb=" O TRP A 289 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE A 286 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 33 through 36 removed outlier: 3.597A pdb=" N GLN B 33 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG B 86 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 229 removed outlier: 6.829A pdb=" N ARG B 243 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL B 266 " --> pdb=" O ARG B 243 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU B 245 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE B 286 " --> pdb=" O GLU B 311 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 708 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: 1.67 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1956 1.34 - 1.46: 1205 1.46 - 1.58: 2774 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 5955 Sorted by residual: bond pdb=" CA PRO A 32 " pdb=" CB PRO A 32 " ideal model delta sigma weight residual 1.533 1.517 0.016 1.80e-02 3.09e+03 7.61e-01 bond pdb=" C ASP B 101 " pdb=" O ASP B 101 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 7.28e-01 bond pdb=" CA ASP B 262 " pdb=" CB ASP B 262 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.47e-01 bond pdb=" CB LYS B 334 " pdb=" CG LYS B 334 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.77e-01 bond pdb=" C ILE B 37 " pdb=" N GLY B 38 " ideal model delta sigma weight residual 1.322 1.331 -0.009 1.20e-02 6.94e+03 5.61e-01 ... (remaining 5950 not shown) Histogram of bond angle deviations from ideal: 99.82 - 106.66: 235 106.66 - 113.50: 3297 113.50 - 120.35: 2083 120.35 - 127.19: 2394 127.19 - 134.03: 110 Bond angle restraints: 8119 Sorted by residual: angle pdb=" C PRO B 261 " pdb=" N ASP B 262 " pdb=" CA ASP B 262 " ideal model delta sigma weight residual 121.54 127.04 -5.50 1.91e+00 2.74e-01 8.29e+00 angle pdb=" CA LYS B 172 " pdb=" CB LYS B 172 " pdb=" CG LYS B 172 " ideal model delta sigma weight residual 114.10 119.61 -5.51 2.00e+00 2.50e-01 7.58e+00 angle pdb=" CA LYS A 172 " pdb=" CB LYS A 172 " pdb=" CG LYS A 172 " ideal model delta sigma weight residual 114.10 119.55 -5.45 2.00e+00 2.50e-01 7.43e+00 angle pdb=" N LYS A 172 " pdb=" CA LYS A 172 " pdb=" C LYS A 172 " ideal model delta sigma weight residual 113.19 109.39 3.80 1.58e+00 4.01e-01 5.79e+00 angle pdb=" CA LYS A 172 " pdb=" C LYS A 172 " pdb=" O LYS A 172 " ideal model delta sigma weight residual 119.08 121.36 -2.28 1.03e+00 9.43e-01 4.91e+00 ... (remaining 8114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3223 17.53 - 35.06: 289 35.06 - 52.58: 54 52.58 - 70.11: 9 70.11 - 87.64: 6 Dihedral angle restraints: 3581 sinusoidal: 1435 harmonic: 2146 Sorted by residual: dihedral pdb=" CA GLU A 57 " pdb=" C GLU A 57 " pdb=" N ASN A 58 " pdb=" CA ASN A 58 " ideal model delta harmonic sigma weight residual 180.00 159.33 20.67 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ARG B 359 " pdb=" C ARG B 359 " pdb=" N GLY B 360 " pdb=" CA GLY B 360 " ideal model delta harmonic sigma weight residual 180.00 163.77 16.23 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CG ARG B 86 " pdb=" CD ARG B 86 " pdb=" NE ARG B 86 " pdb=" CZ ARG B 86 " ideal model delta sinusoidal sigma weight residual 90.00 130.55 -40.55 2 1.50e+01 4.44e-03 9.02e+00 ... (remaining 3578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 654 0.033 - 0.066: 199 0.066 - 0.099: 49 0.099 - 0.132: 11 0.132 - 0.165: 2 Chirality restraints: 915 Sorted by residual: chirality pdb=" CA GLU A 57 " pdb=" N GLU A 57 " pdb=" C GLU A 57 " pdb=" CB GLU A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA ASP B 262 " pdb=" N ASP B 262 " pdb=" C ASP B 262 " pdb=" CB ASP B 262 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 912 not shown) Planarity restraints: 1049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 27 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO B 28 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 3 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO B 4 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 4 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 4 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 53 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C LEU A 53 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU A 53 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG A 54 " 0.008 2.00e-02 2.50e+03 ... (remaining 1046 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1214 2.78 - 3.31: 5637 3.31 - 3.84: 9424 3.84 - 4.37: 10546 4.37 - 4.90: 18185 Nonbonded interactions: 45006 Sorted by model distance: nonbonded pdb=" O GLU B 318 " pdb=" NE2 GLN B 322 " model vdw 2.253 2.520 nonbonded pdb=" OE1 GLU B 331 " pdb=" NZ LYS B 334 " model vdw 2.258 2.520 nonbonded pdb=" OD2 ASP A 186 " pdb=" OG SER A 194 " model vdw 2.261 2.440 nonbonded pdb=" O GLU B 233 " pdb=" OG1 THR B 237 " model vdw 2.267 2.440 nonbonded pdb=" OD2 ASP B 186 " pdb=" OG SER B 194 " model vdw 2.284 2.440 ... (remaining 45001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 325 or resid 335 through 381)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 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: 17.720 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.240 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5955 Z= 0.151 Angle : 0.536 8.768 8119 Z= 0.280 Chirality : 0.035 0.165 915 Planarity : 0.004 0.040 1049 Dihedral : 13.783 87.638 2181 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.14 (0.31), residues: 729 helix: 1.50 (0.30), residues: 342 sheet: -0.39 (0.62), residues: 65 loop : -1.38 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 289 HIS 0.002 0.000 HIS A 280 PHE 0.009 0.001 PHE B 205 TYR 0.005 0.001 TYR B 288 ARG 0.006 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.9104 (mm) cc_final: 0.8739 (mm) REVERT: A 205 PHE cc_start: 0.6997 (m-80) cc_final: 0.6681 (m-10) REVERT: B 85 MET cc_start: 0.7782 (ppp) cc_final: 0.7262 (ppp) REVERT: B 249 ASN cc_start: 0.7516 (t0) cc_final: 0.6903 (t0) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2702 time to fit residues: 46.3367 Evaluate side-chains 73 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 0.0040 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5955 Z= 0.179 Angle : 0.642 13.092 8119 Z= 0.310 Chirality : 0.039 0.161 915 Planarity : 0.004 0.057 1049 Dihedral : 3.768 18.989 798 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.32 % Allowed : 10.71 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.32), residues: 729 helix: 1.36 (0.29), residues: 352 sheet: -0.33 (0.61), residues: 66 loop : -1.05 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 379 HIS 0.003 0.001 HIS A 323 PHE 0.018 0.002 PHE B 350 TYR 0.016 0.003 TYR B 351 ARG 0.010 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8809 (mp0) cc_final: 0.8572 (tp30) REVERT: B 249 ASN cc_start: 0.7563 (t0) cc_final: 0.6949 (t0) outliers start: 8 outliers final: 4 residues processed: 85 average time/residue: 0.2183 time to fit residues: 23.7247 Evaluate side-chains 73 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5955 Z= 0.239 Angle : 0.641 12.979 8119 Z= 0.308 Chirality : 0.039 0.164 915 Planarity : 0.005 0.055 1049 Dihedral : 3.997 18.970 798 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.98 % Allowed : 13.34 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.24 (0.32), residues: 729 helix: 1.28 (0.29), residues: 359 sheet: -0.51 (0.60), residues: 66 loop : -1.03 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 289 HIS 0.004 0.001 HIS B 88 PHE 0.013 0.002 PHE B 224 TYR 0.012 0.002 TYR B 108 ARG 0.005 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 TYR cc_start: 0.7212 (m-80) cc_final: 0.6471 (m-80) REVERT: B 249 ASN cc_start: 0.7609 (t0) cc_final: 0.7066 (t0) outliers start: 12 outliers final: 10 residues processed: 78 average time/residue: 0.1867 time to fit residues: 19.1668 Evaluate side-chains 74 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 167 HIS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 66 optimal weight: 0.0980 chunk 70 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS A 306 HIS ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5955 Z= 0.211 Angle : 0.607 9.914 8119 Z= 0.291 Chirality : 0.038 0.172 915 Planarity : 0.004 0.034 1049 Dihedral : 3.961 18.681 798 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.32 % Allowed : 14.50 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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 (0.32), residues: 729 helix: 1.27 (0.29), residues: 354 sheet: -0.45 (0.62), residues: 66 loop : -0.97 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 289 HIS 0.002 0.001 HIS A 254 PHE 0.014 0.001 PHE B 224 TYR 0.011 0.002 TYR B 108 ARG 0.007 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 249 ASN cc_start: 0.7671 (t0) cc_final: 0.7131 (t0) outliers start: 8 outliers final: 8 residues processed: 72 average time/residue: 0.2050 time to fit residues: 19.1714 Evaluate side-chains 72 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5955 Z= 0.203 Angle : 0.588 8.197 8119 Z= 0.284 Chirality : 0.038 0.167 915 Planarity : 0.004 0.034 1049 Dihedral : 3.868 18.020 798 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.81 % Allowed : 14.83 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.37 (0.33), residues: 729 helix: 1.36 (0.29), residues: 359 sheet: -0.46 (0.61), residues: 66 loop : -0.92 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 289 HIS 0.002 0.001 HIS B 306 PHE 0.015 0.001 PHE B 224 TYR 0.012 0.002 TYR B 108 ARG 0.009 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.9614 (pptt) cc_final: 0.9402 (pptt) REVERT: B 249 ASN cc_start: 0.7714 (t0) cc_final: 0.7155 (t0) REVERT: B 318 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8274 (pm20) outliers start: 11 outliers final: 8 residues processed: 74 average time/residue: 0.1989 time to fit residues: 18.9895 Evaluate side-chains 71 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5955 Z= 0.250 Angle : 0.630 9.442 8119 Z= 0.305 Chirality : 0.039 0.169 915 Planarity : 0.004 0.044 1049 Dihedral : 4.025 19.050 798 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.64 % Allowed : 15.16 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.34 (0.33), residues: 729 helix: 1.31 (0.29), residues: 358 sheet: -0.76 (0.59), residues: 72 loop : -0.82 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 289 HIS 0.002 0.001 HIS B 306 PHE 0.015 0.001 PHE B 224 TYR 0.011 0.002 TYR B 108 ARG 0.004 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 64 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.7718 (mmt) cc_final: 0.7305 (mmm) REVERT: B 225 LYS cc_start: 0.9299 (tptt) cc_final: 0.9086 (tptm) REVERT: B 249 ASN cc_start: 0.7807 (t0) cc_final: 0.7250 (t0) outliers start: 16 outliers final: 8 residues processed: 75 average time/residue: 0.2058 time to fit residues: 19.9142 Evaluate side-chains 69 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5955 Z= 0.192 Angle : 0.603 8.788 8119 Z= 0.290 Chirality : 0.038 0.162 915 Planarity : 0.004 0.032 1049 Dihedral : 3.854 17.839 798 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.81 % Allowed : 17.96 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.42 (0.33), residues: 729 helix: 1.41 (0.29), residues: 359 sheet: -0.44 (0.62), residues: 66 loop : -0.90 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 289 HIS 0.002 0.001 HIS B 306 PHE 0.018 0.001 PHE B 224 TYR 0.012 0.002 TYR B 108 ARG 0.004 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 LYS cc_start: 0.7845 (mmmt) cc_final: 0.7591 (mmmt) REVERT: B 225 LYS cc_start: 0.9295 (tptt) cc_final: 0.9083 (tptm) REVERT: B 249 ASN cc_start: 0.7825 (t0) cc_final: 0.7188 (t0) outliers start: 11 outliers final: 10 residues processed: 74 average time/residue: 0.2053 time to fit residues: 19.7084 Evaluate side-chains 74 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 ASN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5955 Z= 0.213 Angle : 0.609 9.935 8119 Z= 0.294 Chirality : 0.038 0.173 915 Planarity : 0.004 0.053 1049 Dihedral : 3.865 18.494 798 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.81 % Allowed : 18.95 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.48 (0.33), residues: 729 helix: 1.45 (0.29), residues: 359 sheet: -0.47 (0.61), residues: 66 loop : -0.84 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 289 HIS 0.003 0.001 HIS A 210 PHE 0.016 0.002 PHE B 224 TYR 0.012 0.002 TYR B 108 ARG 0.004 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 PHE cc_start: 0.7616 (m-80) cc_final: 0.7195 (m-80) REVERT: B 172 LYS cc_start: 0.7880 (mmmt) cc_final: 0.7611 (mmmt) REVERT: B 225 LYS cc_start: 0.9292 (tptt) cc_final: 0.9084 (tptm) REVERT: B 249 ASN cc_start: 0.7812 (t0) cc_final: 0.7204 (t0) REVERT: B 292 MET cc_start: 0.6031 (mmm) cc_final: 0.5824 (mmm) outliers start: 11 outliers final: 9 residues processed: 76 average time/residue: 0.2307 time to fit residues: 22.4695 Evaluate side-chains 73 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 62 optimal weight: 0.0070 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5955 Z= 0.161 Angle : 0.604 10.573 8119 Z= 0.288 Chirality : 0.038 0.193 915 Planarity : 0.004 0.035 1049 Dihedral : 3.779 19.162 798 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.48 % Allowed : 19.28 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.59 (0.33), residues: 729 helix: 1.54 (0.29), residues: 360 sheet: -0.32 (0.61), residues: 66 loop : -0.84 (0.38), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 289 HIS 0.003 0.001 HIS A 55 PHE 0.018 0.001 PHE B 224 TYR 0.013 0.002 TYR B 108 ARG 0.005 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 LYS cc_start: 0.7843 (mmmt) cc_final: 0.7578 (mmmt) REVERT: B 225 LYS cc_start: 0.9288 (tptt) cc_final: 0.9083 (tptm) REVERT: B 249 ASN cc_start: 0.7804 (t0) cc_final: 0.7153 (t0) outliers start: 9 outliers final: 7 residues processed: 76 average time/residue: 0.2175 time to fit residues: 21.0823 Evaluate side-chains 72 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS A 249 ASN ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5955 Z= 0.187 Angle : 0.646 11.505 8119 Z= 0.306 Chirality : 0.039 0.223 915 Planarity : 0.004 0.035 1049 Dihedral : 3.789 18.463 798 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.48 % Allowed : 19.93 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.49 (0.33), residues: 729 helix: 1.42 (0.29), residues: 365 sheet: -0.37 (0.61), residues: 66 loop : -0.85 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 289 HIS 0.004 0.001 HIS A 210 PHE 0.018 0.001 PHE B 224 TYR 0.012 0.002 TYR B 108 ARG 0.005 0.000 ARG A 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7594 (mmmt) REVERT: B 225 LYS cc_start: 0.9293 (tptt) cc_final: 0.9090 (tptm) REVERT: B 249 ASN cc_start: 0.7804 (t0) cc_final: 0.7223 (t0) outliers start: 9 outliers final: 8 residues processed: 74 average time/residue: 0.2167 time to fit residues: 20.4556 Evaluate side-chains 72 residues out of total 627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** A 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.073796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.052172 restraints weight = 23544.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.053910 restraints weight = 14288.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.055075 restraints weight = 10499.407| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5955 Z= 0.178 Angle : 0.633 11.896 8119 Z= 0.300 Chirality : 0.039 0.193 915 Planarity : 0.004 0.033 1049 Dihedral : 3.731 19.288 798 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.32 % Allowed : 19.60 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: 0.53 (0.33), residues: 729 helix: 1.46 (0.29), residues: 365 sheet: -0.35 (0.61), residues: 66 loop : -0.85 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 289 HIS 0.007 0.001 HIS A 210 PHE 0.019 0.001 PHE B 224 TYR 0.012 0.002 TYR B 108 ARG 0.005 0.000 ARG A 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1844.62 seconds wall clock time: 34 minutes 2.95 seconds (2042.95 seconds total)