Starting phenix.real_space_refine on Fri Nov 15 00:45:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5q_41930/11_2024/8u5q_41930.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5q_41930/11_2024/8u5q_41930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5q_41930/11_2024/8u5q_41930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5q_41930/11_2024/8u5q_41930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5q_41930/11_2024/8u5q_41930.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5q_41930/11_2024/8u5q_41930.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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 46 5.16 5 C 5298 2.51 5 N 1218 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7896 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3935 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 482} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3935 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 482} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.78, per 1000 atoms: 0.73 Number of scatterers: 7896 At special positions: 0 Unit cell: (122.999, 100.837, 76.4589, 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 46 16.00 O 1334 8.00 N 1218 7.00 C 5298 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 - 3.00 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: 2.05 Conformation dependent library (CDL) restraints added in 1.2 seconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.695A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.662A pdb=" N VAL A 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.599A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.660A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 166 through 196 removed outlier: 4.299A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.999A pdb=" N ILE A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 238 through 264 removed outlier: 4.180A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLY A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 326 through 337 removed outlier: 4.190A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.654A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 411 through 433 removed outlier: 3.871A pdb=" N ASN A 417 " --> pdb=" O MET A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 472 Processing helix chain 'A' and resid 655 through 680 removed outlier: 4.265A pdb=" N PHE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA A 671 " --> pdb=" O ILE A 667 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASN A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS A 676 " --> pdb=" O ASN A 672 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 711 removed outlier: 5.676A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 41 through 62 Processing helix chain 'C' and resid 66 through 80 removed outlier: 3.688A pdb=" N LYS C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 93 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.666A pdb=" N VAL C 98 " --> pdb=" O PHE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 125 removed outlier: 3.608A pdb=" N LEU C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 143 Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 149 through 159 removed outlier: 3.660A pdb=" N ILE C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 165 Processing helix chain 'C' and resid 166 through 196 removed outlier: 4.295A pdb=" N TYR C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Proline residue: C 174 - end of helix Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 202 through 216 removed outlier: 4.000A pdb=" N ILE C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 234 Processing helix chain 'C' and resid 238 through 264 removed outlier: 4.180A pdb=" N ASN C 243 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE C 244 " --> pdb=" O TYR C 240 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLY C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 288 Processing helix chain 'C' and resid 288 through 302 Processing helix chain 'C' and resid 306 through 322 Processing helix chain 'C' and resid 326 through 337 removed outlier: 4.195A pdb=" N ALA C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 367 removed outlier: 3.659A pdb=" N ALA C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) Proline residue: C 356 - end of helix Processing helix chain 'C' and resid 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 371 through 404 Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 411 through 433 removed outlier: 3.871A pdb=" N ASN C 417 " --> pdb=" O MET C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 472 Processing helix chain 'C' and resid 655 through 680 removed outlier: 4.294A pdb=" N ILE C 667 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 711 removed outlier: 5.691A pdb=" N GLY C 704 " --> pdb=" O ASN C 700 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N PHE C 705 " --> pdb=" O PHE C 701 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 706 " --> pdb=" O GLY C 702 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1881 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: 2.28 Time building geometry restraints manager: 2.39 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: 2314 1.34 - 1.46: 1845 1.46 - 1.58: 3859 1.58 - 1.70: 0 1.70 - 1.81: 74 Bond restraints: 8092 Sorted by residual: bond pdb=" C1 IAC A 901 " pdb=" C7 IAC A 901 " ideal model delta sigma weight residual 1.433 1.364 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 IAC C 901 " pdb=" C7 IAC C 901 " ideal model delta sigma weight residual 1.433 1.364 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C IAC A 901 " pdb=" C1 IAC A 901 " ideal model delta sigma weight residual 1.414 1.363 0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" C IAC C 901 " pdb=" C1 IAC C 901 " ideal model delta sigma weight residual 1.414 1.365 0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" C17 IAC C 901 " pdb=" C7 IAC C 901 " ideal model delta sigma weight residual 1.487 1.530 -0.043 2.00e-02 2.50e+03 4.68e+00 ... (remaining 8087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 10782 2.71 - 5.42: 186 5.42 - 8.12: 21 8.12 - 10.83: 3 10.83 - 13.54: 4 Bond angle restraints: 10996 Sorted by residual: angle pdb=" C SER A 675 " pdb=" N CYS A 676 " pdb=" CA CYS A 676 " ideal model delta sigma weight residual 121.52 112.76 8.76 1.84e+00 2.95e-01 2.27e+01 angle pdb=" C17 IAC C 901 " pdb=" C7 IAC C 901 " pdb=" C8 IAC C 901 " ideal model delta sigma weight residual 127.34 113.80 13.54 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C17 IAC A 901 " pdb=" C7 IAC A 901 " pdb=" C8 IAC A 901 " ideal model delta sigma weight residual 127.34 113.87 13.47 3.00e+00 1.11e-01 2.02e+01 angle pdb=" C SER C 675 " pdb=" N CYS C 676 " pdb=" CA CYS C 676 " ideal model delta sigma weight residual 120.29 114.59 5.70 1.42e+00 4.96e-01 1.61e+01 angle pdb=" C1 IAC C 901 " pdb=" C7 IAC C 901 " pdb=" C17 IAC C 901 " ideal model delta sigma weight residual 126.92 138.66 -11.74 3.00e+00 1.11e-01 1.53e+01 ... (remaining 10991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4368 16.99 - 33.98: 270 33.98 - 50.98: 37 50.98 - 67.97: 11 67.97 - 84.96: 6 Dihedral angle restraints: 4692 sinusoidal: 1776 harmonic: 2916 Sorted by residual: dihedral pdb=" CA PHE A 670 " pdb=" C PHE A 670 " pdb=" N ALA A 671 " pdb=" CA ALA A 671 " ideal model delta harmonic sigma weight residual -180.00 -151.18 -28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LEU A 233 " pdb=" C LEU A 233 " pdb=" N ASP A 234 " pdb=" CA ASP A 234 " ideal model delta harmonic sigma weight residual -180.00 -153.16 -26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA LEU C 233 " pdb=" C LEU C 233 " pdb=" N ASP C 234 " pdb=" CA ASP C 234 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 4689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 893 0.043 - 0.086: 322 0.086 - 0.128: 79 0.128 - 0.171: 9 0.171 - 0.214: 7 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CA CYS A 676 " pdb=" N CYS A 676 " pdb=" C CYS A 676 " pdb=" CB CYS A 676 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB VAL A 214 " pdb=" CA VAL A 214 " pdb=" CG1 VAL A 214 " pdb=" CG2 VAL A 214 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL C 214 " pdb=" CA VAL C 214 " pdb=" CG1 VAL C 214 " pdb=" CG2 VAL C 214 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1307 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 320 " 0.038 2.00e-02 2.50e+03 2.01e-02 8.10e+00 pdb=" CG TYR A 320 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 320 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 320 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 320 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 320 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 320 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 320 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 320 " 0.038 2.00e-02 2.50e+03 2.00e-02 7.98e+00 pdb=" CG TYR C 320 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C 320 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR C 320 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 320 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 320 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 320 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 320 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 221 " 0.025 2.00e-02 2.50e+03 2.13e-02 7.91e+00 pdb=" CG PHE C 221 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE C 221 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 221 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 221 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 221 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 221 " 0.004 2.00e-02 2.50e+03 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 3119 2.90 - 3.40: 8592 3.40 - 3.90: 14012 3.90 - 4.40: 16360 4.40 - 4.90: 26391 Nonbonded interactions: 68474 Sorted by model distance: nonbonded pdb=" OD1 ASN A 672 " pdb=" ND2 ASN A 700 " model vdw 2.402 3.120 nonbonded pdb=" O LEU C 454 " pdb=" OG1 THR C 457 " model vdw 2.415 3.040 nonbonded pdb=" O LEU A 454 " pdb=" OG1 THR A 457 " model vdw 2.417 3.040 nonbonded pdb=" OH TYR C 359 " pdb=" OD2 ASP C 385 " model vdw 2.417 3.040 nonbonded pdb=" OH TYR A 359 " pdb=" OD2 ASP A 385 " model vdw 2.417 3.040 ... (remaining 68469 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' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.730 Find NCS groups from input model: 0.190 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:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 : 0.006 0.069 8092 Z= 0.357 Angle : 0.896 13.539 10996 Z= 0.477 Chirality : 0.048 0.214 1310 Planarity : 0.006 0.066 1324 Dihedral : 12.123 84.962 2808 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.23 % Allowed : 1.39 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.24), residues: 984 helix: -0.82 (0.16), residues: 804 sheet: None (None), residues: 0 loop : -0.67 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP A 193 HIS 0.014 0.004 HIS A 505 PHE 0.049 0.004 PHE C 221 TYR 0.038 0.004 TYR A 320 ARG 0.004 0.001 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.865 Fit side-chains REVERT: A 41 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7714 (mmm-85) REVERT: A 319 LEU cc_start: 0.8660 (mm) cc_final: 0.8379 (tm) REVERT: A 347 MET cc_start: 0.8783 (tmm) cc_final: 0.8572 (tmm) REVERT: A 455 TYR cc_start: 0.4591 (m-10) cc_final: 0.3607 (t80) REVERT: C 347 MET cc_start: 0.8753 (tmm) cc_final: 0.8533 (tmm) REVERT: C 455 TYR cc_start: 0.4980 (m-10) cc_final: 0.3961 (t80) outliers start: 2 outliers final: 2 residues processed: 187 average time/residue: 1.1250 time to fit residues: 223.5855 Evaluate side-chains 123 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 505 HIS A 672 ASN C 505 HIS C 672 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8092 Z= 0.263 Angle : 0.673 9.273 10996 Z= 0.348 Chirality : 0.045 0.241 1310 Planarity : 0.005 0.034 1324 Dihedral : 5.601 48.418 1060 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.12 % Allowed : 9.47 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.26), residues: 984 helix: 0.93 (0.17), residues: 802 sheet: None (None), residues: 0 loop : -0.29 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 679 HIS 0.008 0.002 HIS A 658 PHE 0.029 0.002 PHE C 221 TYR 0.025 0.002 TYR C 451 ARG 0.004 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.882 Fit side-chains REVERT: A 319 LEU cc_start: 0.8643 (mm) cc_final: 0.8355 (tp) REVERT: A 347 MET cc_start: 0.8545 (tmm) cc_final: 0.8327 (tmm) REVERT: A 455 TYR cc_start: 0.4573 (m-10) cc_final: 0.3643 (t80) REVERT: C 347 MET cc_start: 0.8502 (tmm) cc_final: 0.8288 (tmm) REVERT: C 358 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8221 (mtm) REVERT: C 455 TYR cc_start: 0.4540 (m-10) cc_final: 0.3596 (t80) outliers start: 27 outliers final: 4 residues processed: 169 average time/residue: 1.0044 time to fit residues: 182.3241 Evaluate side-chains 135 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 425 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8092 Z= 0.244 Angle : 0.666 12.689 10996 Z= 0.324 Chirality : 0.043 0.213 1310 Planarity : 0.004 0.034 1324 Dihedral : 4.821 31.966 1058 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 3.58 % Allowed : 12.12 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.27), residues: 984 helix: 1.49 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -0.24 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 679 HIS 0.009 0.002 HIS A 658 PHE 0.029 0.002 PHE C 221 TYR 0.023 0.002 TYR A 451 ARG 0.004 0.000 ARG C 295 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.907 Fit side-chains REVERT: A 41 ARG cc_start: 0.7985 (mtm110) cc_final: 0.7747 (mtm180) REVERT: A 319 LEU cc_start: 0.8667 (mm) cc_final: 0.8346 (tp) REVERT: C 143 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8265 (mp10) outliers start: 31 outliers final: 13 residues processed: 161 average time/residue: 1.0424 time to fit residues: 179.4929 Evaluate side-chains 129 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 658 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 0.0980 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN C 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8092 Z= 0.227 Angle : 0.672 11.025 10996 Z= 0.321 Chirality : 0.042 0.214 1310 Planarity : 0.004 0.034 1324 Dihedral : 4.608 27.856 1058 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.12 % Allowed : 15.36 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.27), residues: 984 helix: 1.67 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -0.26 (0.51), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 679 HIS 0.004 0.001 HIS A 505 PHE 0.029 0.002 PHE C 221 TYR 0.021 0.002 TYR A 451 ARG 0.005 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.906 Fit side-chains REVERT: A 319 LEU cc_start: 0.8668 (mm) cc_final: 0.8316 (tp) outliers start: 27 outliers final: 12 residues processed: 141 average time/residue: 1.1796 time to fit residues: 176.7950 Evaluate side-chains 124 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 511 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN C 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8092 Z= 0.281 Angle : 0.690 11.678 10996 Z= 0.333 Chirality : 0.043 0.226 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.597 26.261 1058 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 3.00 % Allowed : 14.67 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.27), residues: 984 helix: 1.68 (0.18), residues: 802 sheet: None (None), residues: 0 loop : -0.31 (0.51), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 679 HIS 0.003 0.001 HIS C 505 PHE 0.030 0.002 PHE C 221 TYR 0.019 0.002 TYR C 451 ARG 0.005 0.001 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 120 time to evaluate : 0.818 Fit side-chains REVERT: A 319 LEU cc_start: 0.8674 (mm) cc_final: 0.8304 (tp) REVERT: C 143 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8217 (mp10) outliers start: 26 outliers final: 13 residues processed: 133 average time/residue: 1.1890 time to fit residues: 168.0754 Evaluate side-chains 124 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 425 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN C 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8092 Z= 0.276 Angle : 0.701 13.467 10996 Z= 0.335 Chirality : 0.043 0.220 1310 Planarity : 0.004 0.034 1324 Dihedral : 4.604 27.078 1058 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.89 % Allowed : 14.90 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.27), residues: 984 helix: 1.63 (0.18), residues: 814 sheet: None (None), residues: 0 loop : -0.87 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 679 HIS 0.002 0.001 HIS C 505 PHE 0.029 0.002 PHE C 221 TYR 0.021 0.002 TYR C 451 ARG 0.005 0.001 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.918 Fit side-chains REVERT: A 146 ASP cc_start: 0.8385 (m-30) cc_final: 0.8094 (m-30) REVERT: A 319 LEU cc_start: 0.8678 (mm) cc_final: 0.8298 (tp) REVERT: C 143 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8240 (mp10) REVERT: C 358 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8141 (mtm) outliers start: 25 outliers final: 12 residues processed: 131 average time/residue: 1.2571 time to fit residues: 174.3458 Evaluate side-chains 126 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 44 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8092 Z= 0.252 Angle : 0.676 12.327 10996 Z= 0.325 Chirality : 0.043 0.235 1310 Planarity : 0.004 0.034 1324 Dihedral : 4.556 27.584 1058 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.89 % Allowed : 15.36 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.27), residues: 984 helix: 1.71 (0.18), residues: 814 sheet: None (None), residues: 0 loop : -0.91 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 679 HIS 0.002 0.001 HIS A 658 PHE 0.029 0.002 PHE A 221 TYR 0.022 0.002 TYR C 451 ARG 0.005 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.882 Fit side-chains REVERT: A 146 ASP cc_start: 0.8334 (m-30) cc_final: 0.8072 (m-30) REVERT: A 319 LEU cc_start: 0.8656 (mm) cc_final: 0.8261 (tp) REVERT: C 358 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8164 (mtm) outliers start: 25 outliers final: 9 residues processed: 125 average time/residue: 1.2391 time to fit residues: 164.3270 Evaluate side-chains 122 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 400 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 75 optimal weight: 0.2980 chunk 87 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8092 Z= 0.220 Angle : 0.675 12.701 10996 Z= 0.324 Chirality : 0.042 0.271 1310 Planarity : 0.004 0.035 1324 Dihedral : 4.455 28.165 1058 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 3.23 % Allowed : 15.36 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.08 (0.27), residues: 984 helix: 1.84 (0.18), residues: 816 sheet: None (None), residues: 0 loop : -0.87 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 679 HIS 0.002 0.001 HIS A 505 PHE 0.028 0.002 PHE C 221 TYR 0.022 0.002 TYR C 689 ARG 0.006 0.001 ARG C 295 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.903 Fit side-chains REVERT: A 146 ASP cc_start: 0.8283 (m-30) cc_final: 0.8011 (m-30) REVERT: A 319 LEU cc_start: 0.8624 (mm) cc_final: 0.8224 (tp) REVERT: C 358 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8149 (mtm) outliers start: 28 outliers final: 7 residues processed: 132 average time/residue: 1.1895 time to fit residues: 166.7091 Evaluate side-chains 121 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 400 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.0020 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.1980 chunk 94 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN C 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8092 Z= 0.211 Angle : 0.698 14.876 10996 Z= 0.330 Chirality : 0.043 0.305 1310 Planarity : 0.004 0.035 1324 Dihedral : 4.407 27.460 1058 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.08 % Allowed : 17.09 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.16 (0.27), residues: 984 helix: 1.88 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -0.94 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 679 HIS 0.002 0.001 HIS A 658 PHE 0.029 0.002 PHE C 221 TYR 0.025 0.001 TYR C 689 ARG 0.006 0.001 ARG C 295 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.849 Fit side-chains REVERT: C 146 ASP cc_start: 0.8510 (m-30) cc_final: 0.8270 (m-30) outliers start: 18 outliers final: 10 residues processed: 131 average time/residue: 1.2229 time to fit residues: 170.1821 Evaluate side-chains 126 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.0170 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8092 Z= 0.226 Angle : 0.726 15.125 10996 Z= 0.342 Chirality : 0.044 0.324 1310 Planarity : 0.004 0.036 1324 Dihedral : 4.391 27.002 1058 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.96 % Allowed : 17.78 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.15 (0.27), residues: 984 helix: 1.88 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -0.96 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 432 HIS 0.002 0.001 HIS A 658 PHE 0.029 0.002 PHE C 221 TYR 0.023 0.001 TYR C 689 ARG 0.006 0.001 ARG A 295 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.828 Fit side-chains REVERT: C 146 ASP cc_start: 0.8503 (m-30) cc_final: 0.8259 (m-30) outliers start: 17 outliers final: 10 residues processed: 126 average time/residue: 1.2741 time to fit residues: 170.2199 Evaluate side-chains 125 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 419 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.132755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101521 restraints weight = 14408.774| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.48 r_work: 0.3346 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8092 Z= 0.242 Angle : 0.726 14.608 10996 Z= 0.344 Chirality : 0.045 0.327 1310 Planarity : 0.004 0.035 1324 Dihedral : 4.399 26.478 1058 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.73 % Allowed : 18.13 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: 2.09 (0.27), residues: 984 helix: 1.85 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -1.02 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 432 HIS 0.002 0.001 HIS A 658 PHE 0.029 0.002 PHE C 221 TYR 0.022 0.002 TYR C 689 ARG 0.006 0.001 ARG A 295 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3263.43 seconds wall clock time: 59 minutes 19.77 seconds (3559.77 seconds total)