Starting phenix.real_space_refine on Sun Mar 10 23:31:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erp_28557/03_2024/8erp_28557_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erp_28557/03_2024/8erp_28557.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/8erp_28557/03_2024/8erp_28557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erp_28557/03_2024/8erp_28557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erp_28557/03_2024/8erp_28557_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erp_28557/03_2024/8erp_28557_neut_updated.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= 0.023 sd= 0.179 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 4 5.21 5 S 50 5.16 5 C 4074 2.51 5 N 894 2.21 5 O 1028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 90": "OE1" <-> "OE2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6056 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2836 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "A" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2836 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 15, 'TRANS': 348} Chain: "B" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 192 Unusual residues: {' MG': 2, 'CDC': 1, 'LBN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 334 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'LBN:plan-2': 9, 'LBN:plan-3': 9, 'LBN:plan-1': 9} Unresolved non-hydrogen planarities: 93 Chain: "A" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 192 Unusual residues: {' MG': 2, 'CDC': 1, 'LBN': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 334 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'LBN:plan-2': 9, 'LBN:plan-3': 9, 'LBN:plan-1': 9} Unresolved non-hydrogen planarities: 93 Time building chain proxies: 4.08, per 1000 atoms: 0.67 Number of scatterers: 6056 At special positions: 0 Unit cell: (73.7, 115.5, 70.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 6 15.00 Mg 4 11.99 O 1028 8.00 N 894 7.00 C 4074 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: 2.33 Conformation dependent library (CDL) restraints added in 1.3 seconds 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 2 sheets defined 69.8% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'B' and resid 23 through 29 Processing helix chain 'B' and resid 43 through 56 removed outlier: 3.785A pdb=" N LYS B 56 " --> pdb=" O TRP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 84 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 94 through 119 Processing helix chain 'B' and resid 126 through 151 removed outlier: 3.529A pdb=" N MET B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 161 through 179 Processing helix chain 'B' and resid 191 through 208 Processing helix chain 'B' and resid 210 through 214 removed outlier: 3.948A pdb=" N TRP B 213 " --> pdb=" O PRO B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 248 Proline residue: B 228 - end of helix Processing helix chain 'B' and resid 266 through 283 removed outlier: 3.816A pdb=" N HIS B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 292 No H-bonds generated for 'chain 'B' and resid 289 through 292' Processing helix chain 'B' and resid 294 through 317 removed outlier: 3.686A pdb=" N LEU B 312 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 349 through 377 Processing helix chain 'A' and resid 23 through 29 Processing helix chain 'A' and resid 43 through 56 removed outlier: 3.785A pdb=" N LYS A 56 " --> pdb=" O TRP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 84 Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 94 through 119 Processing helix chain 'A' and resid 126 through 151 removed outlier: 3.529A pdb=" N MET A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 191 through 208 Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.948A pdb=" N TRP A 213 " --> pdb=" O PRO A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 248 Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 266 through 283 removed outlier: 3.816A pdb=" N HIS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 292 No H-bonds generated for 'chain 'A' and resid 289 through 292' Processing helix chain 'A' and resid 294 through 317 removed outlier: 3.686A pdb=" N LEU A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 340 Processing helix chain 'A' and resid 349 through 377 Processing sheet with id= A, first strand: chain 'B' and resid 36 through 38 removed outlier: 5.767A pdb=" N LEU B 184 " --> pdb=" O SER B 37 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 36 through 38 removed outlier: 5.767A pdb=" N LEU A 184 " --> pdb=" O SER A 37 " (cutoff:3.500A) No H-bonds generated for sheet with id= B 370 hydrogen bonds defined for protein. 990 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: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 900 1.32 - 1.44: 1620 1.44 - 1.57: 3576 1.57 - 1.69: 12 1.69 - 1.81: 74 Bond restraints: 6182 Sorted by residual: bond pdb=" O3A CDC A 507 " pdb=" PA CDC A 507 " ideal model delta sigma weight residual 1.653 1.592 0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" O3A CDC B 505 " pdb=" PA CDC B 505 " ideal model delta sigma weight residual 1.653 1.592 0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" O1B CDC B 505 " pdb=" PB CDC B 505 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" O1B CDC A 507 " pdb=" PB CDC A 507 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.47e+00 bond pdb=" O2 LBN B 506 " pdb=" P1 LBN B 506 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.27e+00 ... (remaining 6177 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.53: 182 106.53 - 113.39: 3344 113.39 - 120.26: 2374 120.26 - 127.12: 2356 127.12 - 133.99: 68 Bond angle restraints: 8324 Sorted by residual: angle pdb=" O3A CDC A 507 " pdb=" PA CDC A 507 " pdb=" O5' CDC A 507 " ideal model delta sigma weight residual 94.32 105.78 -11.46 3.00e+00 1.11e-01 1.46e+01 angle pdb=" O3A CDC B 505 " pdb=" PA CDC B 505 " pdb=" O5' CDC B 505 " ideal model delta sigma weight residual 94.32 105.78 -11.46 3.00e+00 1.11e-01 1.46e+01 angle pdb=" C TYR A 215 " pdb=" N GLU A 216 " pdb=" CA GLU A 216 " ideal model delta sigma weight residual 121.31 126.84 -5.53 1.49e+00 4.50e-01 1.38e+01 angle pdb=" C TYR B 215 " pdb=" N GLU B 216 " pdb=" CA GLU B 216 " ideal model delta sigma weight residual 121.31 126.84 -5.53 1.49e+00 4.50e-01 1.38e+01 angle pdb=" O1 LBN A 508 " pdb=" P1 LBN A 508 " pdb=" O2 LBN A 508 " ideal model delta sigma weight residual 93.45 104.32 -10.87 3.00e+00 1.11e-01 1.31e+01 ... (remaining 8319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.95: 3456 28.95 - 57.91: 184 57.91 - 86.86: 36 86.86 - 115.82: 4 115.82 - 144.77: 12 Dihedral angle restraints: 3692 sinusoidal: 1590 harmonic: 2102 Sorted by residual: dihedral pdb=" C32 LBN A 513 " pdb=" C33 LBN A 513 " pdb=" C4 LBN A 513 " pdb=" C7 LBN A 513 " ideal model delta sinusoidal sigma weight residual 179.89 -35.34 -144.77 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C32 LBN B 511 " pdb=" C33 LBN B 511 " pdb=" C4 LBN B 511 " pdb=" C7 LBN B 511 " ideal model delta sinusoidal sigma weight residual 179.89 -35.34 -144.77 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" O5 LBN B 506 " pdb=" C2 LBN B 506 " pdb=" C3 LBN B 506 " pdb=" O7 LBN B 506 " ideal model delta sinusoidal sigma weight residual 62.67 -66.11 128.78 1 3.00e+01 1.11e-03 1.73e+01 ... (remaining 3689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 716 0.046 - 0.091: 196 0.091 - 0.137: 28 0.137 - 0.183: 2 0.183 - 0.228: 6 Chirality restraints: 948 Sorted by residual: chirality pdb=" CB ILE B 189 " pdb=" CA ILE B 189 " pdb=" CG1 ILE B 189 " pdb=" CG2 ILE B 189 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE A 189 " pdb=" CA ILE A 189 " pdb=" CG1 ILE A 189 " pdb=" CG2 ILE A 189 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1' CDC B 505 " pdb=" C2' CDC B 505 " pdb=" N1 CDC B 505 " pdb=" O4' CDC B 505 " both_signs ideal model delta sigma weight residual False 2.20 2.42 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 945 not shown) Planarity restraints: 968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C41 LBN A 508 " 0.249 2.00e-02 2.50e+03 2.47e-01 6.08e+02 pdb=" C42 LBN A 508 " -0.255 2.00e-02 2.50e+03 pdb=" C5 LBN A 508 " -0.238 2.00e-02 2.50e+03 pdb=" C8 LBN A 508 " 0.244 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 LBN B 506 " -0.249 2.00e-02 2.50e+03 2.47e-01 6.08e+02 pdb=" C42 LBN B 506 " 0.255 2.00e-02 2.50e+03 pdb=" C5 LBN B 506 " 0.238 2.00e-02 2.50e+03 pdb=" C8 LBN B 506 " -0.244 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 176 " 0.022 2.00e-02 2.50e+03 1.72e-02 7.44e+00 pdb=" CG TRP A 176 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A 176 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 176 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 176 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 176 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 176 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 176 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 176 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 176 " 0.003 2.00e-02 2.50e+03 ... (remaining 965 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 54 2.59 - 3.17: 5210 3.17 - 3.75: 8708 3.75 - 4.32: 11528 4.32 - 4.90: 19501 Nonbonded interactions: 45001 Sorted by model distance: nonbonded pdb=" OD1 ASP A 136 " pdb="MG MG A 503 " model vdw 2.016 2.170 nonbonded pdb=" OD1 ASP B 136 " pdb="MG MG B 501 " model vdw 2.016 2.170 nonbonded pdb=" OD1 ASP B 111 " pdb="MG MG B 501 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP A 111 " pdb="MG MG A 503 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP B 132 " pdb="MG MG B 501 " model vdw 2.067 2.170 ... (remaining 44996 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 383 or (resid 506 and (name C29 or name C30 or \ name C31 or name C32)) or (resid 508 and (name C25 or name C26 or name C27 or na \ me C28 or name C29 or name C30 or name C31 or name C32)) or (resid 509 and (name \ C10 or name C13 or name C26 or name C27 or name C28 or name C29 or name C30 or \ name C31 or name C32 or name C33 or name C4 or name C7 )) or resid 510 through 5 \ 12 or (resid 513 and (name C10 or name C13 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C30 or name C31 or name C32 or name C33 or name C \ 4 or name C7 )))) selection = (chain 'B' and (resid 20 through 383 or (resid 506 and (name C29 or name C30 or \ name C31 or name C32)) or (resid 508 and (name C25 or name C26 or name C27 or na \ me C28 or name C29 or name C30 or name C31 or name C32)) or resid 509 through 51 \ 0 or (resid 511 and (name C10 or name C13 or name C26 or name C27 or name C28 or \ name C29 or name C30 or name C31 or name C32 or name C33 or name C4 or name C7 \ )) or resid 512 through 513)) } 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: 2.900 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: 1.840 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.820 Find NCS groups from input model: 0.380 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6182 Z= 0.285 Angle : 0.855 11.462 8324 Z= 0.452 Chirality : 0.044 0.228 948 Planarity : 0.013 0.247 968 Dihedral : 19.420 144.771 2348 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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 (0.32), residues: 724 helix: 1.54 (0.23), residues: 484 sheet: None (None), residues: 0 loop : -3.07 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 176 HIS 0.004 0.001 HIS B 270 PHE 0.015 0.002 PHE A 171 TYR 0.007 0.001 TYR A 282 ARG 0.002 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.637 Fit side-chains REVERT: B 201 MET cc_start: 0.8097 (ttp) cc_final: 0.7738 (ttm) REVERT: A 201 MET cc_start: 0.8083 (ttp) cc_final: 0.7733 (ttm) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1398 time to fit residues: 22.6730 Evaluate side-chains 100 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 GLN B 293 ASN A 177 GLN A 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6182 Z= 0.211 Angle : 0.641 6.312 8324 Z= 0.340 Chirality : 0.041 0.176 948 Planarity : 0.005 0.040 968 Dihedral : 16.246 109.337 1090 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.27 % Allowed : 13.02 % Favored : 85.71 % 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: 0.37 (0.33), residues: 724 helix: 1.69 (0.23), residues: 490 sheet: None (None), residues: 0 loop : -3.10 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 176 HIS 0.004 0.002 HIS B 270 PHE 0.015 0.002 PHE B 171 TYR 0.013 0.001 TYR A 282 ARG 0.001 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.624 Fit side-chains REVERT: B 201 MET cc_start: 0.8142 (ttp) cc_final: 0.7814 (ttm) REVERT: B 216 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7695 (tm-30) REVERT: A 201 MET cc_start: 0.8127 (ttp) cc_final: 0.7801 (ttm) REVERT: A 216 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7689 (tm-30) outliers start: 8 outliers final: 8 residues processed: 104 average time/residue: 0.1465 time to fit residues: 21.1821 Evaluate side-chains 106 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 316 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 7.9990 chunk 20 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN A 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6182 Z= 0.209 Angle : 0.613 7.765 8324 Z= 0.329 Chirality : 0.041 0.228 948 Planarity : 0.005 0.038 968 Dihedral : 14.366 98.623 1090 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.59 % Allowed : 15.87 % Favored : 82.54 % 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: 0.59 (0.33), residues: 724 helix: 1.86 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -2.95 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 95 HIS 0.004 0.001 HIS B 270 PHE 0.013 0.002 PHE A 165 TYR 0.012 0.001 TYR A 282 ARG 0.001 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 106 time to evaluate : 0.551 Fit side-chains REVERT: B 201 MET cc_start: 0.8097 (ttp) cc_final: 0.7482 (ttm) REVERT: B 216 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7726 (tm-30) REVERT: A 201 MET cc_start: 0.8083 (ttp) cc_final: 0.7472 (ttm) REVERT: A 216 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7724 (tm-30) outliers start: 10 outliers final: 8 residues processed: 110 average time/residue: 0.1358 time to fit residues: 20.8427 Evaluate side-chains 108 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 316 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN A 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6182 Z= 0.185 Angle : 0.604 8.294 8324 Z= 0.322 Chirality : 0.040 0.225 948 Planarity : 0.005 0.039 968 Dihedral : 13.232 94.063 1090 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.54 % Allowed : 18.10 % Favored : 79.37 % 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: 0.76 (0.33), residues: 724 helix: 2.04 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -2.98 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.003 0.001 HIS B 270 PHE 0.014 0.001 PHE B 171 TYR 0.010 0.001 TYR A 282 ARG 0.001 0.000 ARG B 245 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.627 Fit side-chains REVERT: B 201 MET cc_start: 0.8054 (ttp) cc_final: 0.7462 (ttm) REVERT: A 201 MET cc_start: 0.8042 (ttp) cc_final: 0.7453 (ttm) outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 0.1549 time to fit residues: 23.3308 Evaluate side-chains 108 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 316 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN A 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6182 Z= 0.337 Angle : 0.677 6.845 8324 Z= 0.363 Chirality : 0.043 0.179 948 Planarity : 0.005 0.039 968 Dihedral : 13.410 90.624 1090 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.81 % Allowed : 16.83 % Favored : 79.37 % 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: 0.50 (0.33), residues: 724 helix: 1.74 (0.23), residues: 488 sheet: None (None), residues: 0 loop : -2.89 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 176 HIS 0.005 0.001 HIS A 270 PHE 0.018 0.002 PHE A 171 TYR 0.020 0.002 TYR A 282 ARG 0.001 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 0.587 Fit side-chains REVERT: B 55 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7880 (tm-30) REVERT: B 201 MET cc_start: 0.8215 (ttp) cc_final: 0.7786 (ttm) REVERT: B 292 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.6960 (mp10) REVERT: A 55 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 201 MET cc_start: 0.8203 (ttp) cc_final: 0.7776 (ttm) REVERT: A 292 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6961 (mp10) outliers start: 24 outliers final: 20 residues processed: 114 average time/residue: 0.1429 time to fit residues: 22.6207 Evaluate side-chains 116 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 326 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN B 144 ASN A 74 ASN A 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6182 Z= 0.194 Angle : 0.594 6.577 8324 Z= 0.321 Chirality : 0.040 0.172 948 Planarity : 0.005 0.040 968 Dihedral : 12.547 85.940 1090 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.81 % Allowed : 20.00 % Favored : 76.19 % 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: 0.76 (0.33), residues: 724 helix: 2.02 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -2.93 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.004 0.001 HIS B 270 PHE 0.013 0.001 PHE A 171 TYR 0.010 0.001 TYR B 297 ARG 0.001 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 0.622 Fit side-chains REVERT: B 201 MET cc_start: 0.8082 (ttp) cc_final: 0.7355 (ttm) REVERT: B 292 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6902 (mp10) REVERT: A 201 MET cc_start: 0.8067 (ttp) cc_final: 0.7345 (ttm) REVERT: A 292 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.6902 (mp10) outliers start: 24 outliers final: 18 residues processed: 116 average time/residue: 0.1299 time to fit residues: 21.1786 Evaluate side-chains 122 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 342 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN B 144 ASN A 74 ASN A 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6182 Z= 0.211 Angle : 0.612 7.341 8324 Z= 0.328 Chirality : 0.040 0.216 948 Planarity : 0.005 0.039 968 Dihedral : 12.315 82.519 1090 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 3.17 % Allowed : 20.95 % Favored : 75.87 % 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: 0.81 (0.33), residues: 724 helix: 2.05 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -2.91 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 95 HIS 0.004 0.001 HIS A 270 PHE 0.014 0.001 PHE B 171 TYR 0.011 0.001 TYR A 282 ARG 0.001 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.652 Fit side-chains REVERT: B 201 MET cc_start: 0.8103 (ttp) cc_final: 0.7334 (ttm) REVERT: B 292 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6904 (mp10) REVERT: A 201 MET cc_start: 0.8092 (ttp) cc_final: 0.7323 (ttm) REVERT: A 292 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.6902 (mp10) outliers start: 20 outliers final: 16 residues processed: 110 average time/residue: 0.1449 time to fit residues: 22.1809 Evaluate side-chains 118 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 342 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.0270 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN B 144 ASN A 74 ASN A 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6182 Z= 0.184 Angle : 0.588 6.747 8324 Z= 0.314 Chirality : 0.039 0.168 948 Planarity : 0.005 0.039 968 Dihedral : 11.619 74.939 1090 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.49 % Allowed : 20.95 % Favored : 75.56 % 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: 0.97 (0.33), residues: 724 helix: 2.17 (0.23), residues: 488 sheet: None (None), residues: 0 loop : -2.89 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 95 HIS 0.004 0.001 HIS B 270 PHE 0.013 0.001 PHE B 171 TYR 0.009 0.001 TYR B 282 ARG 0.001 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.660 Fit side-chains REVERT: B 201 MET cc_start: 0.8067 (ttp) cc_final: 0.7242 (ttm) REVERT: B 292 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6938 (mp10) REVERT: A 201 MET cc_start: 0.8054 (ttp) cc_final: 0.7233 (ttm) REVERT: A 292 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6938 (mp10) outliers start: 22 outliers final: 16 residues processed: 118 average time/residue: 0.1453 time to fit residues: 24.1625 Evaluate side-chains 116 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 342 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN B 144 ASN A 74 ASN A 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6182 Z= 0.205 Angle : 0.613 7.567 8324 Z= 0.326 Chirality : 0.040 0.219 948 Planarity : 0.005 0.039 968 Dihedral : 11.360 71.216 1090 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.81 % Allowed : 20.95 % Favored : 75.24 % 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: 0.95 (0.33), residues: 724 helix: 2.18 (0.23), residues: 486 sheet: None (None), residues: 0 loop : -2.91 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 176 HIS 0.004 0.001 HIS B 270 PHE 0.014 0.001 PHE A 171 TYR 0.011 0.001 TYR B 282 ARG 0.001 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 0.652 Fit side-chains REVERT: B 201 MET cc_start: 0.8080 (ttp) cc_final: 0.7196 (ttm) REVERT: B 292 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6932 (mp10) REVERT: A 201 MET cc_start: 0.8071 (ttp) cc_final: 0.7187 (ttm) REVERT: A 292 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6938 (mp10) outliers start: 24 outliers final: 16 residues processed: 110 average time/residue: 0.1425 time to fit residues: 21.9535 Evaluate side-chains 112 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain B residue 342 ASN Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 342 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN A 74 ASN A 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6182 Z= 0.248 Angle : 0.656 11.065 8324 Z= 0.343 Chirality : 0.042 0.185 948 Planarity : 0.005 0.039 968 Dihedral : 11.521 76.703 1090 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.86 % Allowed : 22.06 % Favored : 75.08 % 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: 0.86 (0.33), residues: 724 helix: 2.08 (0.23), residues: 488 sheet: None (None), residues: 0 loop : -2.93 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 176 HIS 0.004 0.001 HIS B 270 PHE 0.015 0.002 PHE A 171 TYR 0.019 0.002 TYR A 238 ARG 0.001 0.000 ARG B 245 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1448 Ramachandran restraints generated. 724 Oldfield, 0 Emsley, 724 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.566 Fit side-chains REVERT: B 201 MET cc_start: 0.8124 (ttp) cc_final: 0.7531 (ttm) REVERT: B 292 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.6929 (mp10) REVERT: A 201 MET cc_start: 0.8112 (ttp) cc_final: 0.7521 (ttm) REVERT: A 292 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.6928 (mp10) outliers start: 18 outliers final: 14 residues processed: 105 average time/residue: 0.1432 time to fit residues: 20.9044 Evaluate side-chains 100 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 316 HIS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 316 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN B 144 ASN A 74 ASN A 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.162476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142946 restraints weight = 6700.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141720 restraints weight = 11622.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141451 restraints weight = 11278.774| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6182 Z= 0.203 Angle : 0.662 15.797 8324 Z= 0.337 Chirality : 0.041 0.220 948 Planarity : 0.005 0.039 968 Dihedral : 11.197 77.151 1090 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.86 % Allowed : 22.38 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.33), residues: 724 helix: 2.18 (0.23), residues: 488 sheet: None (None), residues: 0 loop : -2.93 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 176 HIS 0.004 0.001 HIS B 270 PHE 0.015 0.001 PHE A 171 TYR 0.011 0.001 TYR B 282 ARG 0.001 0.000 ARG B 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1285.30 seconds wall clock time: 24 minutes 33.03 seconds (1473.03 seconds total)