Starting phenix.real_space_refine on Sat Dec 9 02:05:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/12_2023/7zlj_14782_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/12_2023/7zlj_14782.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/12_2023/7zlj_14782_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/12_2023/7zlj_14782_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/12_2023/7zlj_14782_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/12_2023/7zlj_14782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/12_2023/7zlj_14782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/12_2023/7zlj_14782_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zlj_14782/12_2023/7zlj_14782_trim_updated.pdb" } resolution = 3.63 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= 0.001 sd= 0.036 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 44 5.16 5 C 6223 2.51 5 N 1593 2.21 5 O 1798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9659 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1679 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1598 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 5352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 662, 5338 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 24, 'TRANS': 637} Conformer: "B" Number of residues, atoms: 662, 5338 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 24, 'TRANS': 637} bond proxies already assigned to first conformer: 5464 Chain: "P" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Unusual residues: {'IZU': 1} Classifications: {'undetermined': 1, 'water': 9} Link IDs: {None: 9} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A 214 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 214 " occ=0.50 Time building chain proxies: 7.84, per 1000 atoms: 0.81 Number of scatterers: 9659 At special positions: 0 Unit cell: (104.94, 165, 99.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 1 15.00 O 1798 8.00 N 1593 7.00 C 6223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 650 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 2.8 seconds 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 13 sheets defined 35.9% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'H' and resid 203 through 206 Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'L' and resid 123 through 126 removed outlier: 3.592A pdb=" N LEU L 126 " --> pdb=" O ASP L 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 123 through 126' Processing helix chain 'L' and resid 184 through 188 removed outlier: 3.524A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 188' Processing helix chain 'A' and resid 26 through 54 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 61 through 67 removed outlier: 4.174A pdb=" N GLU A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N MET A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 84 removed outlier: 4.127A pdb=" N LEU A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 110 through 113 No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 116 through 135 Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 162 through 189 removed outlier: 4.228A pdb=" N THR A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N VAL A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ALA A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 204 Processing helix chain 'A' and resid 220 through 240 Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 245 through 260 removed outlier: 3.753A pdb=" N MET A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 263 through 282 removed outlier: 4.179A pdb=" N PHE A 269 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 273 " --> pdb=" O PHE A 270 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 276 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 277 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 278 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 281 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 307 Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 320 through 336 Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 342 through 368 removed outlier: 3.606A pdb=" N LYS A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 367 " --> pdb=" O GLY A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 removed outlier: 4.087A pdb=" N LEU A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 Processing helix chain 'A' and resid 406 through 415 removed outlier: 3.621A pdb=" N THR A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 434 Processing helix chain 'A' and resid 450 through 468 removed outlier: 3.671A pdb=" N LEU A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 488 Proline residue: A 478 - end of helix removed outlier: 3.769A pdb=" N ALA A 485 " --> pdb=" O CYS A 481 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE A 487 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ALA A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 516 Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 535 through 547 Processing helix chain 'A' and resid 558 through 566 removed outlier: 3.715A pdb=" N ASN A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 594 removed outlier: 4.068A pdb=" N SER A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N MET A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N PHE A 594 " --> pdb=" O VAL A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 632 through 638 removed outlier: 3.881A pdb=" N ASP A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 659 Processing sheet with id= A, first strand: chain 'H' and resid 6 through 10 Processing sheet with id= B, first strand: chain 'H' and resid 13 through 15 removed outlier: 5.714A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 135 through 139 Processing sheet with id= D, first strand: chain 'H' and resid 166 through 169 removed outlier: 4.042A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 3 through 6 removed outlier: 4.117A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 115 through 117 removed outlier: 5.594A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 5 through 7 Processing sheet with id= H, first strand: chain 'L' and resid 11 through 13 removed outlier: 5.598A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'L' and resid 86 through 91 removed outlier: 5.772A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 115 through 119 Processing sheet with id= K, first strand: chain 'L' and resid 193 through 197 Processing sheet with id= L, first strand: chain 'A' and resid 140 through 145 removed outlier: 3.713A pdb=" N LEU A 141 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 157 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 143 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 155 " --> pdb=" O TRP A 143 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 554 through 556 removed outlier: 5.831A pdb=" N TYR A 613 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 674 " --> pdb=" O TYR A 678 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LYS A 682 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE A 670 " --> pdb=" O LYS A 682 " (cutoff:3.500A) 400 hydrogen bonds defined for protein. 1104 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: 3.09 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1613 1.32 - 1.47: 4023 1.47 - 1.61: 4188 1.61 - 1.75: 4 1.75 - 1.90: 67 Bond restraints: 9895 Sorted by residual: bond pdb=" CG PRO H 217 " pdb=" CD PRO H 217 " ideal model delta sigma weight residual 1.503 1.219 0.284 3.40e-02 8.65e+02 6.97e+01 bond pdb=" C PRO A 559 " pdb=" O PRO A 559 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.26e-02 6.30e+03 1.98e+01 bond pdb=" C MET A 558 " pdb=" O MET A 558 " ideal model delta sigma weight residual 1.244 1.209 0.034 9.80e-03 1.04e+04 1.21e+01 bond pdb=" C14 IZU A 801 " pdb=" C15 IZU A 801 " ideal model delta sigma weight residual 1.552 1.614 -0.062 2.00e-02 2.50e+03 9.63e+00 bond pdb=" N VAL A 560 " pdb=" CA VAL A 560 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.63e+00 ... (remaining 9890 not shown) Histogram of bond angle deviations from ideal: 86.80 - 103.20: 88 103.20 - 119.59: 8276 119.59 - 135.99: 5080 135.99 - 152.39: 0 152.39 - 168.79: 2 Bond angle restraints: 13446 Sorted by residual: angle pdb=" C07 IZU A 801 " pdb=" C09 IZU A 801 " pdb=" C10 IZU A 801 " ideal model delta sigma weight residual 112.21 165.07 -52.86 3.00e+00 1.11e-01 3.10e+02 angle pdb=" C12 IZU A 801 " pdb=" C14 IZU A 801 " pdb=" C15 IZU A 801 " ideal model delta sigma weight residual 120.02 168.79 -48.77 3.00e+00 1.11e-01 2.64e+02 angle pdb=" C08 IZU A 801 " pdb=" C07 IZU A 801 " pdb=" C09 IZU A 801 " ideal model delta sigma weight residual 85.87 133.37 -47.50 3.00e+00 1.11e-01 2.51e+02 angle pdb=" C01 IZU A 801 " pdb=" C02 IZU A 801 " pdb=" C03 IZU A 801 " ideal model delta sigma weight residual 74.51 118.84 -44.33 3.00e+00 1.11e-01 2.18e+02 angle pdb=" C06 IZU A 801 " pdb=" C07 IZU A 801 " pdb=" C08 IZU A 801 " ideal model delta sigma weight residual 68.16 105.80 -37.64 3.00e+00 1.11e-01 1.57e+02 ... (remaining 13441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 5705 35.25 - 70.50: 96 70.50 - 105.75: 10 105.75 - 141.00: 0 141.00 - 176.25: 2 Dihedral angle restraints: 5813 sinusoidal: 2242 harmonic: 3571 Sorted by residual: dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual 93.00 34.10 58.90 1 1.00e+01 1.00e-02 4.64e+01 dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 156 " pdb=" CB CYS A 156 " ideal model delta sinusoidal sigma weight residual 93.00 44.99 48.01 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CB CYS A 621 " pdb=" SG CYS A 621 " pdb=" SG CYS A 650 " pdb=" CB CYS A 650 " ideal model delta sinusoidal sigma weight residual -86.00 -43.53 -42.47 1 1.00e+01 1.00e-02 2.52e+01 ... (remaining 5810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 949 0.031 - 0.062: 382 0.062 - 0.093: 108 0.093 - 0.123: 64 0.123 - 0.154: 4 Chirality restraints: 1507 Sorted by residual: chirality pdb=" CA ARG K 19 " pdb=" N ARG K 19 " pdb=" C ARG K 19 " pdb=" CB ARG K 19 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA PRO A 641 " pdb=" N PRO A 641 " pdb=" C PRO A 641 " pdb=" CB PRO A 641 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA PRO A 217 " pdb=" N PRO A 217 " pdb=" C PRO A 217 " pdb=" CB PRO A 217 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1504 not shown) Planarity restraints: 1691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 216 " -0.074 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO H 217 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO H 217 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO H 217 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 640 " 0.062 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO A 641 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 641 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 641 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 163 " -0.038 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO H 164 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO H 164 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 164 " -0.031 5.00e-02 4.00e+02 ... (remaining 1688 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 116 2.61 - 3.18: 8966 3.18 - 3.75: 14289 3.75 - 4.33: 20281 4.33 - 4.90: 33333 Nonbonded interactions: 76985 Sorted by model distance: nonbonded pdb=" OG SER K 17 " pdb=" O MET K 83 " model vdw 2.033 2.440 nonbonded pdb=" NH1 ARG K 53 " pdb=" OG SER K 54 " model vdw 2.070 2.520 nonbonded pdb=" O ILE A 95 " pdb=" OG1 THR A 109 " model vdw 2.083 2.440 nonbonded pdb=" OG1 THR L 130 " pdb=" O LEU L 182 " model vdw 2.086 2.440 nonbonded pdb=" O LYS L 146 " pdb=" OG1 THR L 198 " model vdw 2.102 2.440 ... (remaining 76980 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 13.330 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 33.960 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.005 0.284 9895 Z= 0.342 Angle : 1.151 52.859 13446 Z= 0.479 Chirality : 0.040 0.154 1507 Planarity : 0.005 0.105 1691 Dihedral : 14.366 176.251 3499 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 32.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.77 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.10 (0.25), residues: 1219 helix: 0.91 (0.26), residues: 456 sheet: 0.97 (0.33), residues: 223 loop : -1.07 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 110 HIS 0.003 0.001 HIS A 375 PHE 0.018 0.001 PHE A 430 TYR 0.011 0.001 TYR A 164 ARG 0.009 0.000 ARG K 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.146 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2479 time to fit residues: 42.2499 Evaluate side-chains 97 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 61 optimal weight: 0.0980 chunk 48 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 1 GLN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN A 620 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9895 Z= 0.210 Angle : 0.752 22.257 13446 Z= 0.343 Chirality : 0.045 0.141 1507 Planarity : 0.005 0.049 1691 Dihedral : 8.461 169.076 1350 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.82 % Rotamer: Outliers : 0.76 % Allowed : 5.41 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.30 (0.25), residues: 1219 helix: 1.11 (0.26), residues: 454 sheet: 1.04 (0.31), residues: 249 loop : -1.05 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 262 HIS 0.004 0.001 HIS A 375 PHE 0.040 0.002 PHE A 430 TYR 0.011 0.001 TYR H 60 ARG 0.007 0.001 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 1.347 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 110 average time/residue: 0.2942 time to fit residues: 45.9910 Evaluate side-chains 102 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 98 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1151 time to fit residues: 2.3971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 110 optimal weight: 0.0870 chunk 118 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9895 Z= 0.235 Angle : 0.733 21.725 13446 Z= 0.335 Chirality : 0.044 0.154 1507 Planarity : 0.004 0.042 1691 Dihedral : 8.352 175.584 1350 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.66 % Allowed : 8.45 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1219 helix: 1.00 (0.26), residues: 461 sheet: 1.01 (0.31), residues: 245 loop : -0.99 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 PHE 0.035 0.001 PHE A 430 TYR 0.011 0.001 TYR A 164 ARG 0.004 0.001 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 1.155 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 109 average time/residue: 0.2276 time to fit residues: 35.1795 Evaluate side-chains 103 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2324 time to fit residues: 2.8429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 31 optimal weight: 50.0000 chunk 97 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9895 Z= 0.251 Angle : 0.731 21.566 13446 Z= 0.334 Chirality : 0.044 0.201 1507 Planarity : 0.004 0.038 1691 Dihedral : 8.451 175.207 1350 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.47 % Allowed : 10.35 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1219 helix: 0.97 (0.26), residues: 459 sheet: 1.06 (0.31), residues: 242 loop : -0.96 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 PHE 0.033 0.001 PHE A 487 TYR 0.012 0.001 TYR A 578 ARG 0.005 0.000 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.121 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 107 average time/residue: 0.2490 time to fit residues: 37.2603 Evaluate side-chains 94 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1126 time to fit residues: 1.8930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.004 0.044 9895 Z= 0.238 Angle : 0.731 21.603 13446 Z= 0.333 Chirality : 0.044 0.156 1507 Planarity : 0.004 0.045 1691 Dihedral : 8.414 173.841 1350 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.57 % Allowed : 11.11 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1219 helix: 1.00 (0.26), residues: 459 sheet: 1.00 (0.31), residues: 243 loop : -0.99 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 PHE 0.029 0.001 PHE A 430 TYR 0.010 0.001 TYR A 578 ARG 0.007 0.000 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 1.266 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 105 average time/residue: 0.2205 time to fit residues: 33.0538 Evaluate side-chains 96 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3507 time to fit residues: 2.4649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 9895 Z= 0.454 Angle : 0.829 21.648 13446 Z= 0.392 Chirality : 0.049 0.182 1507 Planarity : 0.005 0.039 1691 Dihedral : 8.646 173.766 1350 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.85 % Allowed : 11.40 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1219 helix: 0.45 (0.25), residues: 452 sheet: 0.82 (0.31), residues: 249 loop : -1.18 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 109 HIS 0.006 0.002 HIS A 375 PHE 0.028 0.002 PHE A 430 TYR 0.017 0.002 TYR A 79 ARG 0.007 0.001 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.358 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 106 average time/residue: 0.2326 time to fit residues: 35.1622 Evaluate side-chains 93 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0967 time to fit residues: 2.0446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9895 Z= 0.180 Angle : 0.725 21.709 13446 Z= 0.327 Chirality : 0.043 0.143 1507 Planarity : 0.004 0.046 1691 Dihedral : 8.325 171.804 1350 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.57 % Allowed : 11.87 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.21 (0.25), residues: 1219 helix: 0.97 (0.26), residues: 458 sheet: 1.04 (0.32), residues: 242 loop : -1.05 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 110 HIS 0.004 0.001 HIS A 479 PHE 0.027 0.001 PHE A 430 TYR 0.009 0.001 TYR A 578 ARG 0.004 0.000 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 109 average time/residue: 0.2405 time to fit residues: 36.8985 Evaluate side-chains 99 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2779 time to fit residues: 2.8179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9895 Z= 0.219 Angle : 0.732 21.794 13446 Z= 0.330 Chirality : 0.043 0.142 1507 Planarity : 0.004 0.037 1691 Dihedral : 8.277 171.908 1350 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.19 % Allowed : 13.01 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.26 (0.25), residues: 1219 helix: 1.05 (0.26), residues: 454 sheet: 1.06 (0.32), residues: 244 loop : -1.05 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 PHE 0.026 0.001 PHE A 430 TYR 0.009 0.001 TYR A 578 ARG 0.005 0.000 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 98 time to evaluate : 1.158 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 100 average time/residue: 0.2507 time to fit residues: 35.1724 Evaluate side-chains 92 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 0.0870 chunk 108 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 138 ASN L 139 ASN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9895 Z= 0.168 Angle : 0.710 21.831 13446 Z= 0.317 Chirality : 0.042 0.139 1507 Planarity : 0.004 0.044 1691 Dihedral : 8.134 170.805 1350 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.28 % Allowed : 13.20 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.44 (0.25), residues: 1219 helix: 1.27 (0.26), residues: 455 sheet: 1.16 (0.32), residues: 243 loop : -1.02 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 110 HIS 0.003 0.001 HIS A 375 PHE 0.025 0.001 PHE A 430 TYR 0.009 0.001 TYR K 110 ARG 0.007 0.000 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.221 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 102 average time/residue: 0.2518 time to fit residues: 36.1053 Evaluate side-chains 95 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 30.0000 chunk 79 optimal weight: 0.3980 chunk 120 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9895 Z= 0.183 Angle : 0.717 21.872 13446 Z= 0.321 Chirality : 0.043 0.137 1507 Planarity : 0.004 0.037 1691 Dihedral : 8.118 171.221 1350 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 0.28 % Allowed : 13.30 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.52 (0.25), residues: 1219 helix: 1.32 (0.26), residues: 455 sheet: 1.25 (0.32), residues: 243 loop : -1.00 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 110 HIS 0.004 0.001 HIS A 375 PHE 0.030 0.001 PHE A 430 TYR 0.010 0.001 TYR K 110 ARG 0.008 0.000 ARG L 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.999 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 93 average time/residue: 0.2504 time to fit residues: 32.7064 Evaluate side-chains 92 residues out of total 1056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1166 time to fit residues: 2.0543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 50.0000 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 ASN ** A 662 ASN ** 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 = 0.4122 r_free = 0.4122 target = 0.168317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.134886 restraints weight = 20102.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135636 restraints weight = 52782.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.136482 restraints weight = 22520.118| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 9895 Z= 0.433 Angle : 0.813 21.903 13446 Z= 0.381 Chirality : 0.048 0.162 1507 Planarity : 0.005 0.040 1691 Dihedral : 8.393 171.046 1350 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.50 % Favored : 93.42 % Rotamer: Outliers : 0.09 % Allowed : 13.39 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: -0.01 (0.24), residues: 1219 helix: 0.74 (0.25), residues: 448 sheet: 1.00 (0.32), residues: 246 loop : -1.15 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 110 HIS 0.006 0.002 HIS A 206 PHE 0.031 0.002 PHE A 430 TYR 0.020 0.002 TYR A 164 ARG 0.008 0.001 ARG L 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2204.80 seconds wall clock time: 41 minutes 3.90 seconds (2463.90 seconds total)