Starting phenix.real_space_refine on Mon Sep 23 23:14:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8n_21575/09_2024/6w8n_21575.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8n_21575/09_2024/6w8n_21575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8n_21575/09_2024/6w8n_21575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8n_21575/09_2024/6w8n_21575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8n_21575/09_2024/6w8n_21575.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w8n_21575/09_2024/6w8n_21575.cif" } resolution = 3.2 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= 0.007 sd= 0.093 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 40 5.16 5 C 4084 2.51 5 N 990 2.21 5 O 1046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6160 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3087 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 383} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3073 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 18, 'TRANS': 383} Chain breaks: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 4.68, per 1000 atoms: 0.76 Number of scatterers: 6160 At special positions: 0 Unit cell: (94.875, 96.525, 78.375, 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 40 16.00 O 1046 8.00 N 990 7.00 C 4084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 196 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 946.5 milliseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.803A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 66 through 99 Processing helix chain 'A' and resid 107 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 136 through 162 removed outlier: 3.990A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.743A pdb=" N SER A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 205 removed outlier: 5.056A pdb=" N GLY A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Proline residue: A 193 - end of helix removed outlier: 3.766A pdb=" N ALA A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 224 removed outlier: 3.621A pdb=" N VAL A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 257 through 274 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.070A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 306 through 334 removed outlier: 3.681A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 363 removed outlier: 3.626A pdb=" N GLY A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 373 through 396 removed outlier: 3.574A pdb=" N ARG A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.818A pdb=" N TRP A 410 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.973A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 459 through 470 removed outlier: 4.025A pdb=" N LEU A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 49 removed outlier: 3.803A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 66 through 99 Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.628A pdb=" N ALA B 110 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 136 through 162 removed outlier: 3.995A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 205 removed outlier: 5.072A pdb=" N GLY B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Proline residue: B 193 - end of helix removed outlier: 3.783A pdb=" N ALA B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 224 removed outlier: 3.614A pdb=" N VAL B 215 " --> pdb=" O TYR B 211 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 257 through 274 Processing helix chain 'B' and resid 274 through 279 removed outlier: 4.062A pdb=" N ASP B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 306 through 334 removed outlier: 3.685A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 363 removed outlier: 3.633A pdb=" N GLY B 342 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 374 through 396 removed outlier: 4.156A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.812A pdb=" N TRP B 410 " --> pdb=" O PRO B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 435 removed outlier: 4.976A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 445 through 470 Proline residue: B 456 - end of helix removed outlier: 4.927A pdb=" N LEU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU B 461 " --> pdb=" O CYS B 457 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1242 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: 1.83 Time building geometry restraints manager: 1.84 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: 1221 1.46 - 1.57: 3144 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 6304 Sorted by residual: bond pdb=" CB VAL B 147 " pdb=" CG1 VAL B 147 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.98e+00 bond pdb=" CB VAL A 147 " pdb=" CG1 VAL A 147 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.96e+00 bond pdb=" CB VAL B 268 " pdb=" CG2 VAL B 268 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.77e+00 bond pdb=" CA ILE A 388 " pdb=" C ILE A 388 " ideal model delta sigma weight residual 1.523 1.504 0.019 1.46e-02 4.69e+03 1.74e+00 bond pdb=" CB VAL A 268 " pdb=" CG2 VAL A 268 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.71e+00 ... (remaining 6299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 8342 1.90 - 3.80: 213 3.80 - 5.71: 39 5.71 - 7.61: 5 7.61 - 9.51: 4 Bond angle restraints: 8603 Sorted by residual: angle pdb=" N SER A 444 " pdb=" CA SER A 444 " pdb=" C SER A 444 " ideal model delta sigma weight residual 112.72 107.66 5.06 1.14e+00 7.69e-01 1.97e+01 angle pdb=" C LEU B 195 " pdb=" N CYS B 196 " pdb=" CA CYS B 196 " ideal model delta sigma weight residual 122.54 117.33 5.21 1.65e+00 3.67e-01 9.98e+00 angle pdb=" C LEU A 195 " pdb=" N CYS A 196 " pdb=" CA CYS A 196 " ideal model delta sigma weight residual 122.54 117.35 5.19 1.65e+00 3.67e-01 9.90e+00 angle pdb=" N LEU B 355 " pdb=" CA LEU B 355 " pdb=" C LEU B 355 " ideal model delta sigma weight residual 113.25 117.24 -3.99 1.30e+00 5.92e-01 9.43e+00 angle pdb=" N LEU A 355 " pdb=" CA LEU A 355 " pdb=" C LEU A 355 " ideal model delta sigma weight residual 113.25 117.22 -3.97 1.30e+00 5.92e-01 9.33e+00 ... (remaining 8598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 3208 17.75 - 35.50: 372 35.50 - 53.25: 96 53.25 - 70.99: 21 70.99 - 88.74: 5 Dihedral angle restraints: 3702 sinusoidal: 1350 harmonic: 2352 Sorted by residual: dihedral pdb=" CB CYS A 144 " pdb=" SG CYS A 144 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -155.42 69.42 1 1.00e+01 1.00e-02 6.23e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual -86.00 -155.27 69.27 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CA GLN B 171 " pdb=" C GLN B 171 " pdb=" N ILE B 172 " pdb=" CA ILE B 172 " ideal model delta harmonic sigma weight residual 180.00 -146.04 -33.96 0 5.00e+00 4.00e-02 4.61e+01 ... (remaining 3699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 668 0.038 - 0.076: 297 0.076 - 0.114: 86 0.114 - 0.152: 13 0.152 - 0.190: 11 Chirality restraints: 1075 Sorted by residual: chirality pdb=" CB THR A 58 " pdb=" CA THR A 58 " pdb=" OG1 THR A 58 " pdb=" CG2 THR A 58 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" CB THR B 58 " pdb=" CA THR B 58 " pdb=" OG1 THR B 58 " pdb=" CG2 THR B 58 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CB VAL B 101 " pdb=" CA VAL B 101 " pdb=" CG1 VAL B 101 " pdb=" CG2 VAL B 101 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 1072 not shown) Planarity restraints: 1044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 307 " 0.028 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 308 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 298 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C SER A 298 " -0.027 2.00e-02 2.50e+03 pdb=" O SER A 298 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 299 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 307 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO B 308 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 308 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 308 " -0.022 5.00e-02 4.00e+02 ... (remaining 1041 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1489 2.78 - 3.31: 6153 3.31 - 3.84: 10410 3.84 - 4.37: 12021 4.37 - 4.90: 20530 Nonbonded interactions: 50603 Sorted by model distance: nonbonded pdb=" O GLN A 171 " pdb=" OG SER A 175 " model vdw 2.244 3.040 nonbonded pdb=" O SER B 444 " pdb=" OG SER B 444 " model vdw 2.257 3.040 nonbonded pdb=" O THR A 306 " pdb=" OG1 THR A 306 " model vdw 2.321 3.040 nonbonded pdb=" O THR B 306 " pdb=" OG1 THR B 306 " model vdw 2.327 3.040 nonbonded pdb=" ND2 ASN A 284 " pdb=" OG1 THR A 306 " model vdw 2.338 3.120 ... (remaining 50598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 through 398 or (resid 3 \ 99 and (name N or name CA or name C or name O or name CB )) or resid 400 through \ 471)) selection = chain 'B' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.870 Find NCS groups from input model: 0.210 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.007 0.047 6304 Z= 0.435 Angle : 0.773 9.512 8603 Z= 0.422 Chirality : 0.048 0.190 1075 Planarity : 0.005 0.041 1044 Dihedral : 16.693 88.743 2160 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 8.14 % Allowed : 21.42 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.74 (0.27), residues: 788 helix: -1.31 (0.19), residues: 604 sheet: None (None), residues: 0 loop : -3.02 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 394 HIS 0.006 0.001 HIS A 328 PHE 0.015 0.002 PHE A 459 TYR 0.016 0.002 TYR A 359 ARG 0.003 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 100 time to evaluate : 0.703 Fit side-chains REVERT: A 101 VAL cc_start: 0.8280 (p) cc_final: 0.8042 (p) REVERT: A 104 LYS cc_start: 0.8459 (mptm) cc_final: 0.8173 (mppt) REVERT: A 336 LYS cc_start: 0.8548 (tttp) cc_final: 0.8263 (tttm) REVERT: A 341 MET cc_start: 0.8079 (mtt) cc_final: 0.7845 (mtt) REVERT: A 390 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: A 448 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.5874 (t80) REVERT: B 104 LYS cc_start: 0.8545 (mptm) cc_final: 0.8218 (mppt) REVERT: B 280 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8317 (mt) REVERT: B 336 LYS cc_start: 0.8578 (tttp) cc_final: 0.8294 (tttm) REVERT: B 341 MET cc_start: 0.8074 (mtt) cc_final: 0.7841 (mtt) outliers start: 54 outliers final: 41 residues processed: 151 average time/residue: 0.1626 time to fit residues: 32.7090 Evaluate side-chains 126 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 82 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.0570 chunk 46 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 191 GLN ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 HIS ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 191 GLN B 284 ASN B 328 HIS B 390 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6304 Z= 0.187 Angle : 0.655 10.281 8603 Z= 0.322 Chirality : 0.043 0.192 1075 Planarity : 0.004 0.043 1044 Dihedral : 10.982 89.326 923 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.03 % Allowed : 25.94 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.29), residues: 788 helix: -0.20 (0.20), residues: 616 sheet: None (None), residues: 0 loop : -2.56 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 324 HIS 0.003 0.001 HIS B 327 PHE 0.018 0.001 PHE A 459 TYR 0.017 0.002 TYR B 313 ARG 0.003 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 85 time to evaluate : 0.818 Fit side-chains REVERT: A 101 VAL cc_start: 0.8178 (p) cc_final: 0.7958 (p) REVERT: A 104 LYS cc_start: 0.8503 (mptm) cc_final: 0.8158 (mptt) REVERT: A 280 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8247 (mt) REVERT: A 336 LYS cc_start: 0.8426 (tttp) cc_final: 0.8154 (tttm) REVERT: A 341 MET cc_start: 0.7953 (mtt) cc_final: 0.7730 (mtt) REVERT: A 394 TRP cc_start: 0.8861 (OUTLIER) cc_final: 0.8430 (t-100) REVERT: A 448 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.5878 (t80) REVERT: A 460 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.5994 (tt) REVERT: B 104 LYS cc_start: 0.8547 (mptm) cc_final: 0.8175 (mptt) REVERT: B 335 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7792 (ptp-170) REVERT: B 336 LYS cc_start: 0.8473 (tttp) cc_final: 0.8165 (tttm) REVERT: B 394 TRP cc_start: 0.8886 (OUTLIER) cc_final: 0.8437 (t-100) outliers start: 40 outliers final: 20 residues processed: 121 average time/residue: 0.1613 time to fit residues: 26.2654 Evaluate side-chains 106 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 80 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 0.0370 chunk 24 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6304 Z= 0.201 Angle : 0.612 9.351 8603 Z= 0.302 Chirality : 0.042 0.226 1075 Planarity : 0.004 0.040 1044 Dihedral : 8.853 62.599 883 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 7.24 % Allowed : 26.09 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.45 (0.30), residues: 788 helix: 0.30 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.26 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 324 HIS 0.004 0.001 HIS A 166 PHE 0.013 0.001 PHE A 459 TYR 0.013 0.002 TYR A 313 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 87 time to evaluate : 0.683 Fit side-chains REVERT: A 101 VAL cc_start: 0.8148 (p) cc_final: 0.7930 (p) REVERT: A 104 LYS cc_start: 0.8402 (mptm) cc_final: 0.8069 (mptt) REVERT: A 280 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8272 (mt) REVERT: A 336 LYS cc_start: 0.8386 (tttp) cc_final: 0.8114 (tttm) REVERT: A 341 MET cc_start: 0.7932 (mtt) cc_final: 0.7715 (mtt) REVERT: A 394 TRP cc_start: 0.8849 (OUTLIER) cc_final: 0.8415 (t-100) REVERT: A 448 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.5926 (t80) REVERT: A 460 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6160 (tt) REVERT: B 104 LYS cc_start: 0.8438 (mptm) cc_final: 0.8070 (mptt) REVERT: B 335 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7877 (ptp-170) REVERT: B 336 LYS cc_start: 0.8402 (tttp) cc_final: 0.8114 (tttm) REVERT: B 394 TRP cc_start: 0.8872 (OUTLIER) cc_final: 0.8390 (t-100) REVERT: B 448 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6208 (t80) outliers start: 48 outliers final: 26 residues processed: 128 average time/residue: 0.1609 time to fit residues: 27.8776 Evaluate side-chains 113 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 80 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 448 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 8 optimal weight: 0.0170 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 73 optimal weight: 0.1980 chunk 77 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6304 Z= 0.172 Angle : 0.592 9.270 8603 Z= 0.288 Chirality : 0.040 0.182 1075 Planarity : 0.004 0.040 1044 Dihedral : 8.204 59.923 878 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 7.09 % Allowed : 25.64 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.06 (0.30), residues: 788 helix: 0.75 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.43 (0.43), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 PHE 0.012 0.001 PHE A 459 TYR 0.014 0.002 TYR B 313 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 82 time to evaluate : 0.818 Fit side-chains REVERT: A 101 VAL cc_start: 0.8109 (p) cc_final: 0.7902 (p) REVERT: A 104 LYS cc_start: 0.8357 (mptm) cc_final: 0.8044 (mptt) REVERT: A 280 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8236 (mt) REVERT: A 336 LYS cc_start: 0.8286 (tttp) cc_final: 0.8039 (tttm) REVERT: A 341 MET cc_start: 0.7882 (mtt) cc_final: 0.7657 (mtt) REVERT: A 394 TRP cc_start: 0.8841 (OUTLIER) cc_final: 0.8387 (t-100) REVERT: A 448 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.5970 (t80) REVERT: A 460 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6157 (tt) REVERT: B 104 LYS cc_start: 0.8417 (mptm) cc_final: 0.8076 (mptt) REVERT: B 335 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7692 (ptp-170) REVERT: B 336 LYS cc_start: 0.8362 (tttp) cc_final: 0.8059 (tttm) REVERT: B 373 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6478 (mp) REVERT: B 394 TRP cc_start: 0.8842 (OUTLIER) cc_final: 0.8370 (t-100) REVERT: B 448 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6110 (t80) outliers start: 47 outliers final: 26 residues processed: 121 average time/residue: 0.1552 time to fit residues: 25.6335 Evaluate side-chains 112 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 78 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 448 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.0030 chunk 1 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6304 Z= 0.215 Angle : 0.595 9.203 8603 Z= 0.294 Chirality : 0.041 0.206 1075 Planarity : 0.004 0.039 1044 Dihedral : 7.569 59.799 871 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 6.94 % Allowed : 26.09 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.28 (0.31), residues: 788 helix: 0.82 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.01 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 PHE 0.011 0.001 PHE A 459 TYR 0.013 0.002 TYR B 359 ARG 0.001 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 74 time to evaluate : 0.721 Fit side-chains REVERT: A 101 VAL cc_start: 0.8120 (p) cc_final: 0.7915 (p) REVERT: A 104 LYS cc_start: 0.8335 (mptm) cc_final: 0.7991 (mptt) REVERT: A 280 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8278 (mt) REVERT: A 336 LYS cc_start: 0.8321 (tttp) cc_final: 0.8073 (tttm) REVERT: A 341 MET cc_start: 0.7933 (mtt) cc_final: 0.7727 (mtt) REVERT: A 394 TRP cc_start: 0.8844 (OUTLIER) cc_final: 0.8379 (t-100) REVERT: A 448 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.6129 (t80) REVERT: A 460 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6156 (tt) REVERT: B 104 LYS cc_start: 0.8397 (mptm) cc_final: 0.8052 (mptt) REVERT: B 335 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7794 (ptp-170) REVERT: B 336 LYS cc_start: 0.8392 (tttp) cc_final: 0.8071 (tttm) REVERT: B 373 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6460 (mp) REVERT: B 394 TRP cc_start: 0.8866 (OUTLIER) cc_final: 0.8371 (t-100) REVERT: B 448 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6106 (t80) REVERT: B 451 MET cc_start: 0.6846 (tmm) cc_final: 0.6584 (tmm) outliers start: 46 outliers final: 26 residues processed: 115 average time/residue: 0.1589 time to fit residues: 24.8765 Evaluate side-chains 106 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 72 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 448 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 74 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6304 Z= 0.183 Angle : 0.596 9.089 8603 Z= 0.293 Chirality : 0.040 0.219 1075 Planarity : 0.004 0.038 1044 Dihedral : 7.451 59.935 869 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 7.09 % Allowed : 26.24 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.31), residues: 788 helix: 1.00 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.30 (0.43), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 PHE 0.029 0.001 PHE B 459 TYR 0.014 0.002 TYR A 313 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 79 time to evaluate : 0.597 Fit side-chains REVERT: A 101 VAL cc_start: 0.8084 (p) cc_final: 0.7881 (p) REVERT: A 104 LYS cc_start: 0.8310 (mptm) cc_final: 0.7971 (mptt) REVERT: A 280 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8197 (mt) REVERT: A 336 LYS cc_start: 0.8271 (tttp) cc_final: 0.8039 (tttm) REVERT: A 341 MET cc_start: 0.7916 (mtt) cc_final: 0.7697 (mtt) REVERT: A 394 TRP cc_start: 0.8855 (OUTLIER) cc_final: 0.8379 (t-100) REVERT: A 448 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6088 (t80) REVERT: A 460 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.6055 (tt) REVERT: B 104 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7991 (mptt) REVERT: B 335 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7755 (ptp-170) REVERT: B 336 LYS cc_start: 0.8380 (tttp) cc_final: 0.8082 (tttm) REVERT: B 373 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6504 (mp) REVERT: B 394 TRP cc_start: 0.8859 (OUTLIER) cc_final: 0.8358 (t-100) REVERT: B 448 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.5642 (t80) REVERT: B 451 MET cc_start: 0.6833 (tmm) cc_final: 0.6546 (tmm) REVERT: B 452 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6256 (mp10) outliers start: 47 outliers final: 26 residues processed: 119 average time/residue: 0.1587 time to fit residues: 25.6999 Evaluate side-chains 111 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 75 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6304 Z= 0.202 Angle : 0.610 9.028 8603 Z= 0.295 Chirality : 0.041 0.230 1075 Planarity : 0.004 0.061 1044 Dihedral : 7.367 59.718 869 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 7.39 % Allowed : 26.40 % Favored : 66.21 % 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: 0.51 (0.31), residues: 788 helix: 1.00 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.95 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 PHE 0.022 0.001 PHE B 459 TYR 0.013 0.002 TYR B 313 ARG 0.001 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 77 time to evaluate : 0.620 Fit side-chains REVERT: A 101 VAL cc_start: 0.8091 (p) cc_final: 0.7888 (p) REVERT: A 104 LYS cc_start: 0.8315 (mptm) cc_final: 0.7975 (mptt) REVERT: A 280 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8245 (mt) REVERT: A 336 LYS cc_start: 0.8289 (tttp) cc_final: 0.8059 (tttm) REVERT: A 341 MET cc_start: 0.7933 (mtt) cc_final: 0.7726 (mtt) REVERT: A 394 TRP cc_start: 0.8868 (OUTLIER) cc_final: 0.8371 (t-100) REVERT: A 448 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.6170 (t80) REVERT: A 460 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.6130 (tt) REVERT: B 104 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8003 (mptt) REVERT: B 335 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7763 (ptp-170) REVERT: B 336 LYS cc_start: 0.8387 (tttp) cc_final: 0.8088 (tttm) REVERT: B 394 TRP cc_start: 0.8879 (OUTLIER) cc_final: 0.8354 (t-100) REVERT: B 448 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.5618 (t80) REVERT: B 451 MET cc_start: 0.6813 (tmm) cc_final: 0.6526 (tmm) REVERT: B 452 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6286 (mp10) outliers start: 49 outliers final: 30 residues processed: 118 average time/residue: 0.1546 time to fit residues: 24.8626 Evaluate side-chains 115 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 76 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 73 optimal weight: 0.0970 chunk 67 optimal weight: 4.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6304 Z= 0.178 Angle : 0.607 9.003 8603 Z= 0.294 Chirality : 0.040 0.239 1075 Planarity : 0.004 0.059 1044 Dihedral : 7.261 59.961 869 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 6.33 % Allowed : 27.60 % Favored : 66.06 % 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: 0.58 (0.31), residues: 788 helix: 1.11 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.23 (0.43), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS A 327 PHE 0.018 0.001 PHE B 459 TYR 0.014 0.001 TYR A 313 ARG 0.002 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 80 time to evaluate : 0.665 Fit side-chains REVERT: A 101 VAL cc_start: 0.8156 (p) cc_final: 0.7938 (p) REVERT: A 104 LYS cc_start: 0.8281 (mptm) cc_final: 0.7960 (mptt) REVERT: A 341 MET cc_start: 0.7895 (mtt) cc_final: 0.7686 (mtt) REVERT: A 359 TYR cc_start: 0.8187 (OUTLIER) cc_final: 0.6760 (t80) REVERT: A 394 TRP cc_start: 0.8844 (OUTLIER) cc_final: 0.8359 (t-100) REVERT: A 448 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6293 (t80) REVERT: B 104 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7966 (mptt) REVERT: B 335 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7641 (ptp-170) REVERT: B 336 LYS cc_start: 0.8364 (tttp) cc_final: 0.8062 (tttm) REVERT: B 359 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.6786 (t80) REVERT: B 394 TRP cc_start: 0.8871 (OUTLIER) cc_final: 0.8343 (t-100) REVERT: B 448 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.5623 (t80) REVERT: B 451 MET cc_start: 0.6793 (tmm) cc_final: 0.6527 (tmm) REVERT: B 452 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6283 (mp10) outliers start: 42 outliers final: 29 residues processed: 113 average time/residue: 0.1569 time to fit residues: 24.2041 Evaluate side-chains 116 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 78 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 43 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 22 optimal weight: 0.0970 chunk 64 optimal weight: 0.0670 chunk 67 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6304 Z= 0.158 Angle : 0.592 8.913 8603 Z= 0.285 Chirality : 0.039 0.239 1075 Planarity : 0.004 0.056 1044 Dihedral : 7.036 59.489 869 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 6.49 % Allowed : 28.05 % Favored : 65.46 % 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: 0.71 (0.31), residues: 788 helix: 1.22 (0.22), residues: 614 sheet: None (None), residues: 0 loop : -2.24 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 324 HIS 0.003 0.001 HIS B 327 PHE 0.014 0.001 PHE B 459 TYR 0.012 0.001 TYR B 313 ARG 0.002 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 86 time to evaluate : 0.667 Fit side-chains REVERT: A 104 LYS cc_start: 0.8217 (mptm) cc_final: 0.7908 (mptt) REVERT: A 359 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.6732 (t80) REVERT: A 394 TRP cc_start: 0.8823 (OUTLIER) cc_final: 0.8294 (t-100) REVERT: A 448 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6358 (t80) REVERT: B 104 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7936 (mppt) REVERT: B 336 LYS cc_start: 0.8330 (tttp) cc_final: 0.8033 (tttm) REVERT: B 359 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.6788 (t80) REVERT: B 394 TRP cc_start: 0.8858 (OUTLIER) cc_final: 0.8347 (t-100) REVERT: B 448 PHE cc_start: 0.7204 (OUTLIER) cc_final: 0.6092 (t80) REVERT: B 451 MET cc_start: 0.6800 (tmm) cc_final: 0.6591 (tmm) outliers start: 43 outliers final: 29 residues processed: 120 average time/residue: 0.1505 time to fit residues: 24.7084 Evaluate side-chains 120 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 84 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.0270 chunk 52 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 73 optimal weight: 0.1980 chunk 63 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6304 Z= 0.180 Angle : 0.605 8.999 8603 Z= 0.292 Chirality : 0.040 0.254 1075 Planarity : 0.004 0.056 1044 Dihedral : 6.853 59.619 863 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.58 % Allowed : 28.96 % Favored : 65.46 % 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: 0.70 (0.30), residues: 788 helix: 1.18 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.13 (0.42), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 PHE 0.014 0.001 PHE B 459 TYR 0.012 0.001 TYR A 313 ARG 0.002 0.000 ARG A 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 85 time to evaluate : 0.691 Fit side-chains REVERT: A 104 LYS cc_start: 0.8229 (mptm) cc_final: 0.7920 (mptt) REVERT: A 359 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.6724 (t80) REVERT: A 394 TRP cc_start: 0.8837 (OUTLIER) cc_final: 0.8388 (t-100) REVERT: A 448 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6385 (t80) REVERT: B 104 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7893 (mptt) REVERT: B 336 LYS cc_start: 0.8369 (tttp) cc_final: 0.8069 (tttm) REVERT: B 359 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.6758 (t80) REVERT: B 394 TRP cc_start: 0.8874 (OUTLIER) cc_final: 0.8356 (t-100) REVERT: B 448 PHE cc_start: 0.7195 (OUTLIER) cc_final: 0.5648 (t80) REVERT: B 451 MET cc_start: 0.6815 (tmm) cc_final: 0.6585 (tmm) REVERT: B 452 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6231 (mp10) outliers start: 37 outliers final: 27 residues processed: 114 average time/residue: 0.1551 time to fit residues: 24.0851 Evaluate side-chains 120 residues out of total 678 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 85 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 394 TRP Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain B residue 104 LYS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 359 TYR Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 394 TRP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 452 GLN Chi-restraints excluded: chain B residue 455 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 GLN ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.157159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.125034 restraints weight = 7269.174| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.97 r_work: 0.3183 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6304 Z= 0.178 Angle : 0.605 8.957 8603 Z= 0.292 Chirality : 0.040 0.259 1075 Planarity : 0.004 0.055 1044 Dihedral : 6.831 59.177 863 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.88 % Allowed : 28.96 % Favored : 65.16 % 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 (0.30), residues: 788 helix: 1.25 (0.21), residues: 614 sheet: None (None), residues: 0 loop : -2.20 (0.42), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS A 166 PHE 0.014 0.001 PHE B 459 TYR 0.013 0.001 TYR B 313 ARG 0.005 0.000 ARG A 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1609.96 seconds wall clock time: 29 minutes 13.67 seconds (1753.67 seconds total)