Starting phenix.real_space_refine on Tue Feb 13 11:11:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymd_33927/02_2024/7ymd_33927.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymd_33927/02_2024/7ymd_33927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.176 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymd_33927/02_2024/7ymd_33927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymd_33927/02_2024/7ymd_33927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymd_33927/02_2024/7ymd_33927.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymd_33927/02_2024/7ymd_33927.pdb" } resolution = 4.176 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= 0.007 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 25 5.16 5 C 3575 2.51 5 N 969 2.21 5 O 1084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 287": "OE1" <-> "OE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 15": "OD1" <-> "OD2" Residue "C ASP 159": "OD1" <-> "OD2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5653 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 816 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2573 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2264 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Time building chain proxies: 3.73, per 1000 atoms: 0.66 Number of scatterers: 5653 At special positions: 0 Unit cell: (77.256, 83.52, 99.18, 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 25 16.00 O 1084 8.00 N 969 7.00 C 3575 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: 2.19 Conformation dependent library (CDL) restraints added in 980.0 milliseconds 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 5 sheets defined 50.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.523A pdb=" N ARG A 202 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS A 203 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR A 205 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN A 207 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLN A 208 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 210 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS A 211 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 227 removed outlier: 4.243A pdb=" N ILE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 27 removed outlier: 3.529A pdb=" N ALA B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 49 removed outlier: 5.015A pdb=" N ASP B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 77 removed outlier: 4.064A pdb=" N LEU B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 97 removed outlier: 4.346A pdb=" N LYS B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 168 Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.881A pdb=" N GLU B 186 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 223 through 237 Processing helix chain 'B' and resid 251 through 258 removed outlier: 3.575A pdb=" N ILE B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 266 Processing helix chain 'B' and resid 306 through 316 Processing helix chain 'C' and resid 8 through 25 removed outlier: 4.549A pdb=" N LEU C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 42 removed outlier: 4.054A pdb=" N ARG C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 63 Processing helix chain 'C' and resid 68 through 83 Processing helix chain 'C' and resid 94 through 99 removed outlier: 4.030A pdb=" N ASN C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 146 removed outlier: 3.522A pdb=" N PHE C 138 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR C 146 " --> pdb=" O GLN C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 151 removed outlier: 3.744A pdb=" N ILE C 151 " --> pdb=" O TYR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 Processing helix chain 'C' and resid 177 through 195 Processing helix chain 'C' and resid 201 through 209 Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' Processing helix chain 'C' and resid 226 through 237 Processing helix chain 'C' and resid 259 through 266 Processing helix chain 'C' and resid 267 through 280 Processing helix chain 'C' and resid 282 through 287 removed outlier: 4.455A pdb=" N LYS C 287 " --> pdb=" O GLU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 298 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 33 removed outlier: 3.573A pdb=" N CYS B 32 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 133 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.194A pdb=" N SER B 207 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 281 " --> pdb=" O VAL B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 240 through 242 Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 47 removed outlier: 4.690A pdb=" N LYS C 122 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE C 124 " --> pdb=" O GLN C 89 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 89 " --> pdb=" O ILE C 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 199 through 200 removed outlier: 3.954A pdb=" N ILE C 199 " --> pdb=" O TYR C 256 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 669 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: 1.25 Time building geometry restraints manager: 2.40 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: 1877 1.34 - 1.46: 874 1.46 - 1.58: 2954 1.58 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 5744 Sorted by residual: bond pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ASP C 7 " pdb=" CA ASP C 7 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ASN B 286 " pdb=" CA ASN B 286 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.99e-01 bond pdb=" CB GLU B 45 " pdb=" CG GLU B 45 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.84e-01 bond pdb=" N THR C 168 " pdb=" CA THR C 168 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.69e-01 ... (remaining 5739 not shown) Histogram of bond angle deviations from ideal: 100.22 - 106.97: 87 106.97 - 113.72: 3221 113.72 - 120.48: 2211 120.48 - 127.23: 2191 127.23 - 133.98: 40 Bond angle restraints: 7750 Sorted by residual: angle pdb=" C ASN B 286 " pdb=" CA ASN B 286 " pdb=" CB ASN B 286 " ideal model delta sigma weight residual 110.42 115.61 -5.19 1.99e+00 2.53e-01 6.81e+00 angle pdb=" C TYR A 212 " pdb=" N ASN A 213 " pdb=" CA ASN A 213 " ideal model delta sigma weight residual 121.54 125.73 -4.19 1.91e+00 2.74e-01 4.81e+00 angle pdb=" C LYS C 196 " pdb=" N ASN C 197 " pdb=" CA ASN C 197 " ideal model delta sigma weight residual 121.54 125.46 -3.92 1.91e+00 2.74e-01 4.20e+00 angle pdb=" C THR C 168 " pdb=" CA THR C 168 " pdb=" CB THR C 168 " ideal model delta sigma weight residual 110.42 114.48 -4.06 1.99e+00 2.53e-01 4.15e+00 angle pdb=" C ARG A 127 " pdb=" CA ARG A 127 " pdb=" CB ARG A 127 " ideal model delta sigma weight residual 109.54 112.83 -3.29 1.84e+00 2.95e-01 3.19e+00 ... (remaining 7745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3220 17.94 - 35.88: 219 35.88 - 53.82: 40 53.82 - 71.76: 7 71.76 - 89.69: 3 Dihedral angle restraints: 3489 sinusoidal: 1422 harmonic: 2067 Sorted by residual: dihedral pdb=" CA ARG A 127 " pdb=" C ARG A 127 " pdb=" N SER A 128 " pdb=" CA SER A 128 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA CYS B 32 " pdb=" C CYS B 32 " pdb=" N HIS B 33 " pdb=" CA HIS B 33 " ideal model delta harmonic sigma weight residual -180.00 -163.01 -16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA MET B 265 " pdb=" C MET B 265 " pdb=" N TYR B 266 " pdb=" CA TYR B 266 " ideal model delta harmonic sigma weight residual 180.00 163.73 16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 3486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 562 0.025 - 0.050: 190 0.050 - 0.075: 73 0.075 - 0.100: 34 0.100 - 0.125: 25 Chirality restraints: 884 Sorted by residual: chirality pdb=" CA VAL C 129 " pdb=" N VAL C 129 " pdb=" C VAL C 129 " pdb=" CB VAL C 129 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA ILE C 254 " pdb=" N ILE C 254 " pdb=" C ILE C 254 " pdb=" CB ILE C 254 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 881 not shown) Planarity restraints: 993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 160 " 0.009 2.00e-02 2.50e+03 7.84e-03 1.54e+00 pdb=" CG TRP B 160 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP B 160 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 160 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 160 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 160 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 160 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 160 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 160 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 160 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 242 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO A 243 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 196 " 0.005 2.00e-02 2.50e+03 1.11e-02 1.22e+00 pdb=" C LYS C 196 " -0.019 2.00e-02 2.50e+03 pdb=" O LYS C 196 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN C 197 " 0.006 2.00e-02 2.50e+03 ... (remaining 990 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 79 2.60 - 3.18: 5545 3.18 - 3.75: 8420 3.75 - 4.33: 11466 4.33 - 4.90: 18681 Nonbonded interactions: 44191 Sorted by model distance: nonbonded pdb=" O SER B 213 " pdb=" OG1 THR B 214 " model vdw 2.026 2.440 nonbonded pdb=" OE2 GLU A 214 " pdb=" CG GLN A 217 " model vdw 2.216 3.440 nonbonded pdb=" O LEU C 80 " pdb=" N GLY C 85 " model vdw 2.219 2.520 nonbonded pdb=" OH TYR B 20 " pdb=" O PRO C 130 " model vdw 2.247 2.440 nonbonded pdb=" O LYS C 287 " pdb=" OG SER C 288 " model vdw 2.263 2.440 ... (remaining 44186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.950 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.840 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 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 0.033 5744 Z= 0.131 Angle : 0.481 5.193 7750 Z= 0.278 Chirality : 0.037 0.125 884 Planarity : 0.002 0.028 993 Dihedral : 12.735 89.694 2145 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 0.16 (0.35), residues: 693 helix: 1.35 (0.31), residues: 330 sheet: -0.54 (1.16), residues: 22 loop : -1.13 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 160 HIS 0.007 0.001 HIS C 56 PHE 0.015 0.001 PHE B 165 TYR 0.008 0.001 TYR B 261 ARG 0.005 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 MET cc_start: 0.8043 (tpp) cc_final: 0.7781 (tpp) REVERT: B 222 LEU cc_start: 0.8632 (mm) cc_final: 0.7899 (tp) REVERT: C 197 ASN cc_start: 0.7333 (p0) cc_final: 0.7112 (p0) REVERT: C 224 ASN cc_start: 0.8580 (m-40) cc_final: 0.8119 (t0) REVERT: C 257 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7442 (tpt-90) REVERT: C 299 ASP cc_start: 0.7148 (p0) cc_final: 0.6436 (p0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1408 time to fit residues: 33.5053 Evaluate side-chains 145 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 20 optimal weight: 0.0980 chunk 32 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN C 145 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5744 Z= 0.250 Angle : 0.600 9.623 7750 Z= 0.314 Chirality : 0.042 0.141 884 Planarity : 0.003 0.035 993 Dihedral : 4.246 19.718 757 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % 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: -0.27 (0.34), residues: 693 helix: 0.80 (0.29), residues: 335 sheet: -1.73 (0.96), residues: 26 loop : -1.05 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 160 HIS 0.009 0.002 HIS A 147 PHE 0.015 0.002 PHE B 248 TYR 0.014 0.002 TYR B 135 ARG 0.003 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9122 (mtmm) cc_final: 0.8913 (mtmm) REVERT: A 241 MET cc_start: 0.6061 (pmm) cc_final: 0.5799 (pmm) REVERT: B 163 GLU cc_start: 0.8598 (tt0) cc_final: 0.8150 (mm-30) REVERT: B 222 LEU cc_start: 0.8647 (mm) cc_final: 0.8048 (tp) REVERT: C 31 MET cc_start: 0.8699 (tpp) cc_final: 0.8276 (tpp) REVERT: C 139 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8573 (tttt) REVERT: C 148 GLU cc_start: 0.8406 (pt0) cc_final: 0.7841 (pt0) REVERT: C 197 ASN cc_start: 0.7794 (p0) cc_final: 0.7579 (p0) REVERT: C 277 GLU cc_start: 0.8329 (pp20) cc_final: 0.8093 (pp20) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1572 time to fit residues: 36.5190 Evaluate side-chains 140 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 9.9990 chunk 19 optimal weight: 0.0370 chunk 52 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN C 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5744 Z= 0.253 Angle : 0.607 8.621 7750 Z= 0.319 Chirality : 0.042 0.185 884 Planarity : 0.003 0.035 993 Dihedral : 4.408 22.128 757 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 0.32 % Allowed : 3.50 % Favored : 96.18 % 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: -0.63 (0.33), residues: 693 helix: 0.44 (0.29), residues: 338 sheet: -2.07 (0.93), residues: 26 loop : -1.14 (0.37), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 160 HIS 0.006 0.001 HIS C 56 PHE 0.019 0.002 PHE C 135 TYR 0.012 0.002 TYR A 227 ARG 0.003 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 MET cc_start: 0.6462 (pmm) cc_final: 0.6070 (pmm) REVERT: B 33 HIS cc_start: 0.8881 (t70) cc_final: 0.8613 (t-90) REVERT: B 158 MET cc_start: 0.8331 (tpp) cc_final: 0.8050 (tpp) REVERT: B 163 GLU cc_start: 0.8575 (tt0) cc_final: 0.8065 (mm-30) REVERT: C 48 ARG cc_start: 0.8579 (tpt-90) cc_final: 0.8110 (mmm160) REVERT: C 237 ARG cc_start: 0.9046 (mtt180) cc_final: 0.8607 (ttm170) outliers start: 2 outliers final: 2 residues processed: 177 average time/residue: 0.1778 time to fit residues: 41.1843 Evaluate side-chains 147 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 29 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5744 Z= 0.239 Angle : 0.608 11.623 7750 Z= 0.319 Chirality : 0.042 0.170 884 Planarity : 0.003 0.035 993 Dihedral : 4.565 22.879 757 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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 (0.33), residues: 693 helix: 0.39 (0.28), residues: 336 sheet: -2.12 (0.93), residues: 26 loop : -1.16 (0.37), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 160 HIS 0.009 0.002 HIS A 147 PHE 0.023 0.002 PHE C 207 TYR 0.022 0.002 TYR A 227 ARG 0.003 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8092 (mmm) cc_final: 0.7316 (tpp) REVERT: A 133 GLU cc_start: 0.8322 (tp30) cc_final: 0.8063 (tp30) REVERT: A 143 MET cc_start: 0.5488 (ttt) cc_final: 0.5259 (ttt) REVERT: A 241 MET cc_start: 0.6634 (pmm) cc_final: 0.6184 (pmm) REVERT: B 33 HIS cc_start: 0.8834 (t70) cc_final: 0.8547 (t-90) REVERT: B 261 TYR cc_start: 0.8190 (t80) cc_final: 0.7882 (t80) REVERT: C 31 MET cc_start: 0.8695 (tpp) cc_final: 0.8030 (tpp) REVERT: C 48 ARG cc_start: 0.8541 (tpt-90) cc_final: 0.8152 (tpt-90) REVERT: C 237 ARG cc_start: 0.9049 (mtt180) cc_final: 0.8670 (ttm170) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1618 time to fit residues: 36.4980 Evaluate side-chains 139 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 chunk 34 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN C 56 HIS C 89 GLN C 118 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5744 Z= 0.206 Angle : 0.592 8.546 7750 Z= 0.306 Chirality : 0.042 0.156 884 Planarity : 0.003 0.038 993 Dihedral : 4.614 23.444 757 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: -0.69 (0.33), residues: 693 helix: 0.40 (0.29), residues: 337 sheet: -2.26 (0.94), residues: 26 loop : -1.18 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 160 HIS 0.007 0.001 HIS C 56 PHE 0.019 0.002 PHE C 207 TYR 0.017 0.002 TYR A 227 ARG 0.004 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8296 (mmm) cc_final: 0.8061 (tpp) REVERT: A 133 GLU cc_start: 0.8331 (tp30) cc_final: 0.8079 (tp30) REVERT: A 237 THR cc_start: 0.9338 (p) cc_final: 0.8970 (p) REVERT: B 158 MET cc_start: 0.8313 (tpp) cc_final: 0.7835 (mmm) REVERT: B 207 SER cc_start: 0.8281 (t) cc_final: 0.7833 (p) REVERT: C 31 MET cc_start: 0.8833 (tpp) cc_final: 0.8251 (tpp) REVERT: C 40 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6574 (mt-10) REVERT: C 139 LYS cc_start: 0.8819 (tttt) cc_final: 0.8618 (tttm) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1592 time to fit residues: 35.4905 Evaluate side-chains 144 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 0.0050 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 7 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5744 Z= 0.154 Angle : 0.582 9.861 7750 Z= 0.304 Chirality : 0.041 0.151 884 Planarity : 0.003 0.040 993 Dihedral : 4.458 23.902 757 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % 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: -0.62 (0.33), residues: 693 helix: 0.52 (0.29), residues: 337 sheet: -2.02 (0.99), residues: 26 loop : -1.25 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 160 HIS 0.007 0.001 HIS C 56 PHE 0.018 0.002 PHE C 207 TYR 0.021 0.002 TYR B 313 ARG 0.005 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8314 (tp30) cc_final: 0.8053 (tp30) REVERT: A 215 PHE cc_start: 0.6931 (t80) cc_final: 0.6660 (t80) REVERT: A 237 THR cc_start: 0.9229 (p) cc_final: 0.8884 (p) REVERT: B 33 HIS cc_start: 0.8621 (t70) cc_final: 0.8352 (t-90) REVERT: B 261 TYR cc_start: 0.8016 (t80) cc_final: 0.7762 (t80) REVERT: B 305 TRP cc_start: 0.5885 (m-90) cc_final: 0.5208 (m-90) REVERT: C 31 MET cc_start: 0.8843 (tpp) cc_final: 0.8327 (tpp) REVERT: C 40 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6204 (mt-10) REVERT: C 149 GLU cc_start: 0.8271 (mp0) cc_final: 0.8047 (mp0) REVERT: C 197 ASN cc_start: 0.7398 (p0) cc_final: 0.7188 (p0) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1552 time to fit residues: 35.8206 Evaluate side-chains 149 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 0.0770 chunk 30 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS C 290 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5744 Z= 0.165 Angle : 0.600 10.441 7750 Z= 0.306 Chirality : 0.042 0.157 884 Planarity : 0.003 0.041 993 Dihedral : 4.479 23.955 757 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.33), residues: 693 helix: 0.49 (0.29), residues: 338 sheet: -2.00 (1.01), residues: 26 loop : -1.36 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 160 HIS 0.007 0.001 HIS C 56 PHE 0.019 0.001 PHE C 207 TYR 0.022 0.002 TYR B 261 ARG 0.003 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8306 (tp30) cc_final: 0.8043 (tp30) REVERT: A 143 MET cc_start: 0.5379 (ttt) cc_final: 0.5069 (ttt) REVERT: A 226 LEU cc_start: 0.8201 (mp) cc_final: 0.7842 (mp) REVERT: A 228 ASN cc_start: 0.7621 (t0) cc_final: 0.7333 (t0) REVERT: A 237 THR cc_start: 0.9326 (p) cc_final: 0.8931 (p) REVERT: B 33 HIS cc_start: 0.8639 (t70) cc_final: 0.8335 (t-90) REVERT: B 265 MET cc_start: 0.8885 (tmm) cc_final: 0.8679 (tmm) REVERT: B 305 TRP cc_start: 0.5843 (m-90) cc_final: 0.5229 (m-90) REVERT: C 31 MET cc_start: 0.8845 (tpp) cc_final: 0.8168 (tpp) REVERT: C 40 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6403 (mt-10) REVERT: C 149 GLU cc_start: 0.8047 (mp0) cc_final: 0.7720 (mp0) REVERT: C 262 THR cc_start: 0.8187 (m) cc_final: 0.7985 (m) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1588 time to fit residues: 37.1740 Evaluate side-chains 145 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS C 290 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5744 Z= 0.209 Angle : 0.621 8.804 7750 Z= 0.318 Chirality : 0.042 0.162 884 Planarity : 0.003 0.042 993 Dihedral : 4.628 23.934 757 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -0.75 (0.33), residues: 693 helix: 0.46 (0.29), residues: 337 sheet: -1.86 (0.98), residues: 26 loop : -1.38 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 160 HIS 0.007 0.002 HIS C 56 PHE 0.021 0.002 PHE A 215 TYR 0.024 0.002 TYR B 313 ARG 0.003 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8310 (tp30) cc_final: 0.8049 (tp30) REVERT: A 226 LEU cc_start: 0.8174 (mp) cc_final: 0.7803 (mp) REVERT: A 237 THR cc_start: 0.9227 (p) cc_final: 0.8940 (p) REVERT: B 207 SER cc_start: 0.8396 (t) cc_final: 0.8013 (p) REVERT: B 305 TRP cc_start: 0.5755 (m-90) cc_final: 0.5129 (m-90) REVERT: C 31 MET cc_start: 0.8887 (tpp) cc_final: 0.8336 (tpp) REVERT: C 40 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6665 (mt-10) REVERT: C 72 MET cc_start: 0.8336 (tpt) cc_final: 0.7924 (tpp) REVERT: C 262 THR cc_start: 0.8171 (m) cc_final: 0.7964 (m) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1546 time to fit residues: 34.2043 Evaluate side-chains 143 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN C 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5744 Z= 0.170 Angle : 0.636 9.272 7750 Z= 0.317 Chirality : 0.042 0.146 884 Planarity : 0.003 0.042 993 Dihedral : 4.612 24.182 757 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -0.83 (0.33), residues: 693 helix: 0.30 (0.29), residues: 346 sheet: -1.83 (1.01), residues: 26 loop : -1.36 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 160 HIS 0.008 0.001 HIS C 56 PHE 0.022 0.002 PHE A 215 TYR 0.023 0.002 TYR B 261 ARG 0.004 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8288 (tp30) cc_final: 0.8042 (tp30) REVERT: A 226 LEU cc_start: 0.8101 (mp) cc_final: 0.7661 (mp) REVERT: A 244 LEU cc_start: 0.9151 (tp) cc_final: 0.8905 (tp) REVERT: B 33 HIS cc_start: 0.8684 (t70) cc_final: 0.8483 (t-90) REVERT: B 261 TYR cc_start: 0.8087 (t80) cc_final: 0.7853 (t80) REVERT: B 268 LEU cc_start: 0.9065 (tp) cc_final: 0.8857 (tp) REVERT: B 305 TRP cc_start: 0.5639 (m-90) cc_final: 0.5061 (m-90) REVERT: C 31 MET cc_start: 0.8817 (tpp) cc_final: 0.8209 (tpp) REVERT: C 72 MET cc_start: 0.8282 (tpt) cc_final: 0.7970 (tpp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1541 time to fit residues: 34.5776 Evaluate side-chains 144 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN C 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5744 Z= 0.206 Angle : 0.650 12.272 7750 Z= 0.325 Chirality : 0.043 0.147 884 Planarity : 0.004 0.042 993 Dihedral : 4.709 23.993 757 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -0.92 (0.32), residues: 693 helix: 0.21 (0.29), residues: 342 sheet: -1.83 (1.01), residues: 26 loop : -1.37 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 160 HIS 0.008 0.002 HIS C 56 PHE 0.016 0.002 PHE C 207 TYR 0.031 0.002 TYR A 227 ARG 0.005 0.000 ARG C 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8283 (tp30) cc_final: 0.8056 (tp30) REVERT: A 226 LEU cc_start: 0.8151 (mp) cc_final: 0.7712 (mp) REVERT: B 33 HIS cc_start: 0.8691 (t70) cc_final: 0.8007 (t-90) REVERT: B 207 SER cc_start: 0.8401 (t) cc_final: 0.8045 (p) REVERT: B 260 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7514 (tp30) REVERT: B 305 TRP cc_start: 0.5661 (m-90) cc_final: 0.5126 (m-90) REVERT: C 31 MET cc_start: 0.8860 (tpp) cc_final: 0.8183 (tpp) REVERT: C 72 MET cc_start: 0.8320 (tpt) cc_final: 0.7974 (tpp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1461 time to fit residues: 32.2237 Evaluate side-chains 140 residues out of total 633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 22 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN C 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.195328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.151964 restraints weight = 9024.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157231 restraints weight = 5848.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.160965 restraints weight = 4367.338| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5744 Z= 0.165 Angle : 0.619 9.328 7750 Z= 0.316 Chirality : 0.042 0.145 884 Planarity : 0.003 0.043 993 Dihedral : 4.673 24.304 757 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.83 (0.33), residues: 693 helix: 0.37 (0.29), residues: 344 sheet: -1.86 (1.00), residues: 26 loop : -1.43 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 160 HIS 0.008 0.002 HIS C 56 PHE 0.025 0.002 PHE A 215 TYR 0.023 0.002 TYR B 313 ARG 0.003 0.000 ARG B 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1423.47 seconds wall clock time: 26 minutes 47.27 seconds (1607.27 seconds total)