Starting phenix.real_space_refine on Thu Mar 6 07:06:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8inb_35595/03_2025/8inb_35595_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8inb_35595/03_2025/8inb_35595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8inb_35595/03_2025/8inb_35595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8inb_35595/03_2025/8inb_35595.map" model { file = "/net/cci-nas-00/data/ceres_data/8inb_35595/03_2025/8inb_35595_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8inb_35595/03_2025/8inb_35595_neut.cif" } resolution = 3.1 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= 0.014 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 65 5.49 5 S 8 5.16 5 C 3141 2.51 5 N 969 2.21 5 O 1138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5321 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3966 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 37, 'TRANS': 460} Chain breaks: 2 Chain: "B" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 753 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 8, 'rna3p_pur': 11, 'rna3p_pyr': 16} Link IDs: {'rna2p': 9, 'rna3p': 26} Chain: "C" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 463 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 139 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 5.16, per 1000 atoms: 0.97 Number of scatterers: 5321 At special positions: 0 Unit cell: (85.8, 90.42, 97.02, 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 8 16.00 P 65 15.00 O 1138 8.00 N 969 7.00 C 3141 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: 1.52 Conformation dependent library (CDL) restraints added in 627.1 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 932 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 49.8% alpha, 9.8% beta 19 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.832A pdb=" N GLY A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 99 removed outlier: 4.178A pdb=" N GLU A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 125 through 168 removed outlier: 6.611A pdb=" N LEU A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.782A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.569A pdb=" N ARG A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 367 through 380 removed outlier: 4.291A pdb=" N LYS A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 450 removed outlier: 3.553A pdb=" N GLN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 464 removed outlier: 3.745A pdb=" N GLU A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 558 removed outlier: 4.182A pdb=" N ALA A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 587 removed outlier: 3.503A pdb=" N ARG A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 removed outlier: 3.958A pdb=" N LEU A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ALA A 639 " --> pdb=" O PHE A 635 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.793A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN A 64 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLN A 68 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TRP A 304 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 420 removed outlier: 5.958A pdb=" N PHE A 401 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLN A 418 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA A 399 " --> pdb=" O GLN A 418 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A 384 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY A 385 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL A 595 " --> pdb=" O GLY A 385 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 387 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE A 647 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE A 594 " --> pdb=" O ILE A 647 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1308 1.33 - 1.45: 1320 1.45 - 1.57: 2804 1.57 - 1.69: 126 1.69 - 1.81: 11 Bond restraints: 5569 Sorted by residual: bond pdb=" O3' DT D -2 " pdb=" P DT D -1 " ideal model delta sigma weight residual 1.607 1.568 0.039 1.50e-02 4.44e+03 6.74e+00 bond pdb=" O3' DT D -1 " pdb=" P DC D 0 " ideal model delta sigma weight residual 1.607 1.578 0.029 1.50e-02 4.44e+03 3.72e+00 bond pdb=" CA GLU A 380 " pdb=" CB GLU A 380 " ideal model delta sigma weight residual 1.527 1.545 -0.019 1.44e-02 4.82e+03 1.67e+00 bond pdb=" CA VAL A 207 " pdb=" C VAL A 207 " ideal model delta sigma weight residual 1.524 1.515 0.010 1.05e-02 9.07e+03 8.25e-01 bond pdb=" CA HIS A 253 " pdb=" CB HIS A 253 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.31e-02 5.83e+03 7.37e-01 ... (remaining 5564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 7616 1.58 - 3.16: 187 3.16 - 4.73: 23 4.73 - 6.31: 4 6.31 - 7.89: 3 Bond angle restraints: 7833 Sorted by residual: angle pdb=" O3' DC D 0 " pdb=" C3' DC D 0 " pdb=" C2' DC D 0 " ideal model delta sigma weight residual 111.50 103.61 7.89 1.50e+00 4.44e-01 2.77e+01 angle pdb=" O3' DT D -1 " pdb=" C3' DT D -1 " pdb=" C2' DT D -1 " ideal model delta sigma weight residual 111.50 104.60 6.90 1.50e+00 4.44e-01 2.11e+01 angle pdb=" C3' DC D 0 " pdb=" C2' DC D 0 " pdb=" C1' DC D 0 " ideal model delta sigma weight residual 101.60 106.69 -5.09 1.50e+00 4.44e-01 1.15e+01 angle pdb=" C3' DT D -1 " pdb=" C2' DT D -1 " pdb=" C1' DT D -1 " ideal model delta sigma weight residual 101.60 106.48 -4.88 1.50e+00 4.44e-01 1.06e+01 angle pdb=" CA GLU A 380 " pdb=" CB GLU A 380 " pdb=" CG GLU A 380 " ideal model delta sigma weight residual 114.10 120.33 -6.23 2.00e+00 2.50e-01 9.71e+00 ... (remaining 7828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 3078 35.58 - 71.16: 291 71.16 - 106.74: 23 106.74 - 142.32: 0 142.32 - 177.89: 1 Dihedral angle restraints: 3393 sinusoidal: 1953 harmonic: 1440 Sorted by residual: dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual 232.00 54.11 177.89 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' G B 11 " pdb=" C1' G B 11 " pdb=" N9 G B 11 " pdb=" C4 G B 11 " ideal model delta sinusoidal sigma weight residual -106.00 -154.63 48.63 1 1.70e+01 3.46e-03 1.13e+01 dihedral pdb=" CG ARG A 115 " pdb=" CD ARG A 115 " pdb=" NE ARG A 115 " pdb=" CZ ARG A 115 " ideal model delta sinusoidal sigma weight residual -180.00 -135.93 -44.07 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 3390 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 670 0.037 - 0.073: 163 0.073 - 0.110: 47 0.110 - 0.147: 14 0.147 - 0.184: 4 Chirality restraints: 898 Sorted by residual: chirality pdb=" C3' DT D -1 " pdb=" C4' DT D -1 " pdb=" O3' DT D -1 " pdb=" C2' DT D -1 " both_signs ideal model delta sigma weight residual False -2.66 -2.84 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" C1' DT D -1 " pdb=" O4' DT D -1 " pdb=" C2' DT D -1 " pdb=" N1 DT D -1 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CA ASN A 234 " pdb=" N ASN A 234 " pdb=" C ASN A 234 " pdb=" CB ASN A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 895 not shown) Planarity restraints: 775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 210 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO A 211 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 223 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO A 224 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 224 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 224 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 242 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO A 243 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.031 5.00e-02 4.00e+02 ... (remaining 772 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 990 2.77 - 3.30: 4776 3.30 - 3.83: 9288 3.83 - 4.37: 10863 4.37 - 4.90: 17091 Nonbonded interactions: 43008 Sorted by model distance: nonbonded pdb=" OG SER A 361 " pdb=" O LEU A 640 " model vdw 2.235 3.040 nonbonded pdb=" O PRO A 224 " pdb=" OG SER A 327 " model vdw 2.252 3.040 nonbonded pdb=" OG SER A 105 " pdb=" OG SER A 108 " model vdw 2.278 3.040 nonbonded pdb=" N GLY A 183 " pdb=" O LYS A 187 " model vdw 2.289 3.120 nonbonded pdb=" NH1 ARG A 70 " pdb=" OD1 ASP A 303 " model vdw 2.292 3.120 ... (remaining 43003 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.430 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 : 0.003 0.039 5569 Z= 0.187 Angle : 0.589 7.890 7833 Z= 0.334 Chirality : 0.039 0.184 898 Planarity : 0.006 0.066 775 Dihedral : 22.430 177.895 2461 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.24 % Allowed : 27.19 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.39), residues: 492 helix: 1.23 (0.36), residues: 216 sheet: -1.34 (0.67), residues: 62 loop : -0.78 (0.45), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.021 0.002 HIS A 253 PHE 0.006 0.001 PHE A 102 TYR 0.017 0.001 TYR A 432 ARG 0.003 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.516 Fit side-chains REVERT: A 549 ASP cc_start: 0.6896 (m-30) cc_final: 0.6690 (m-30) outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.3048 time to fit residues: 12.6625 Evaluate side-chains 32 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.0010 chunk 49 optimal weight: 2.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS A 383 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.163126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121533 restraints weight = 6928.890| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.76 r_work: 0.3329 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5569 Z= 0.242 Angle : 0.567 5.643 7833 Z= 0.303 Chirality : 0.039 0.127 898 Planarity : 0.006 0.054 775 Dihedral : 23.009 178.999 1449 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.65 % Allowed : 26.48 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.40), residues: 492 helix: 1.65 (0.36), residues: 217 sheet: -1.72 (0.60), residues: 70 loop : -0.78 (0.46), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 249 HIS 0.013 0.002 HIS A 253 PHE 0.009 0.001 PHE A 137 TYR 0.019 0.001 TYR A 432 ARG 0.005 0.000 ARG A 556 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.463 Fit side-chains REVERT: A 549 ASP cc_start: 0.7765 (m-30) cc_final: 0.7268 (m-30) outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 0.2668 time to fit residues: 14.7841 Evaluate side-chains 37 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 547 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 12 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.0370 chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.167924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126419 restraints weight = 6959.357| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.82 r_work: 0.3378 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5569 Z= 0.152 Angle : 0.513 5.267 7833 Z= 0.273 Chirality : 0.036 0.125 898 Planarity : 0.005 0.047 775 Dihedral : 22.721 178.859 1449 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.18 % Allowed : 26.95 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.40), residues: 492 helix: 1.92 (0.36), residues: 217 sheet: -1.45 (0.62), residues: 69 loop : -0.70 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 318 HIS 0.001 0.000 HIS A 383 PHE 0.007 0.001 PHE A 137 TYR 0.017 0.001 TYR A 432 ARG 0.007 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.494 Fit side-chains REVERT: A 549 ASP cc_start: 0.7726 (m-30) cc_final: 0.7256 (m-30) outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.2527 time to fit residues: 14.0997 Evaluate side-chains 38 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.167157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125545 restraints weight = 7144.539| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.80 r_work: 0.3365 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5569 Z= 0.169 Angle : 0.512 4.791 7833 Z= 0.272 Chirality : 0.037 0.131 898 Planarity : 0.005 0.045 775 Dihedral : 22.677 178.883 1449 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.13 % Allowed : 25.77 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.40), residues: 492 helix: 2.01 (0.36), residues: 217 sheet: -1.46 (0.62), residues: 69 loop : -0.64 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 249 HIS 0.001 0.000 HIS A 383 PHE 0.008 0.001 PHE A 137 TYR 0.017 0.001 TYR A 432 ARG 0.013 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.488 Fit side-chains REVERT: A 549 ASP cc_start: 0.7707 (m-30) cc_final: 0.7251 (m-30) outliers start: 9 outliers final: 6 residues processed: 43 average time/residue: 0.2465 time to fit residues: 13.1870 Evaluate side-chains 40 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 210 ASN Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 24 optimal weight: 0.0970 chunk 41 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122647 restraints weight = 7038.386| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.80 r_work: 0.3329 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5569 Z= 0.229 Angle : 0.537 4.716 7833 Z= 0.284 Chirality : 0.038 0.133 898 Planarity : 0.005 0.046 775 Dihedral : 22.719 179.375 1449 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.60 % Allowed : 25.53 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.40), residues: 492 helix: 2.06 (0.35), residues: 215 sheet: -1.46 (0.62), residues: 68 loop : -0.60 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 249 HIS 0.001 0.000 HIS A 383 PHE 0.009 0.001 PHE A 350 TYR 0.017 0.001 TYR A 432 ARG 0.006 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.520 Fit side-chains REVERT: A 544 ARG cc_start: 0.7331 (tpt170) cc_final: 0.6720 (tpp-160) REVERT: A 549 ASP cc_start: 0.7717 (m-30) cc_final: 0.7265 (m-30) outliers start: 11 outliers final: 9 residues processed: 44 average time/residue: 0.2681 time to fit residues: 14.5499 Evaluate side-chains 42 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.164695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.122814 restraints weight = 7025.987| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.80 r_work: 0.3333 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5569 Z= 0.215 Angle : 0.528 4.686 7833 Z= 0.279 Chirality : 0.038 0.139 898 Planarity : 0.005 0.045 775 Dihedral : 22.692 179.029 1449 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.36 % Allowed : 24.82 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.40), residues: 492 helix: 2.14 (0.35), residues: 215 sheet: -1.47 (0.61), residues: 68 loop : -0.59 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 249 HIS 0.001 0.000 HIS A 121 PHE 0.009 0.001 PHE A 137 TYR 0.016 0.001 TYR A 432 ARG 0.010 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.455 Fit side-chains REVERT: A 372 GLU cc_start: 0.8498 (tp30) cc_final: 0.8213 (tp30) REVERT: A 544 ARG cc_start: 0.7346 (tpt170) cc_final: 0.6759 (tpp-160) REVERT: A 549 ASP cc_start: 0.7733 (m-30) cc_final: 0.7295 (m-30) outliers start: 10 outliers final: 8 residues processed: 45 average time/residue: 0.2507 time to fit residues: 14.0562 Evaluate side-chains 43 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 0.0170 chunk 36 optimal weight: 0.9980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.165096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122762 restraints weight = 7052.725| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.89 r_work: 0.3324 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5569 Z= 0.163 Angle : 0.506 4.623 7833 Z= 0.268 Chirality : 0.037 0.158 898 Planarity : 0.005 0.044 775 Dihedral : 22.553 178.594 1449 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.65 % Allowed : 26.00 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.40), residues: 492 helix: 2.26 (0.35), residues: 215 sheet: -1.32 (0.61), residues: 68 loop : -0.52 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 249 HIS 0.001 0.000 HIS A 383 PHE 0.008 0.001 PHE A 137 TYR 0.017 0.001 TYR A 432 ARG 0.008 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.495 Fit side-chains REVERT: A 372 GLU cc_start: 0.8526 (tp30) cc_final: 0.8234 (tp30) REVERT: A 544 ARG cc_start: 0.7309 (tpt170) cc_final: 0.6739 (tpp-160) REVERT: A 549 ASP cc_start: 0.7697 (m-30) cc_final: 0.7262 (m-30) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.2511 time to fit residues: 12.7047 Evaluate side-chains 42 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.121324 restraints weight = 7045.141| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.93 r_work: 0.3302 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5569 Z= 0.264 Angle : 0.553 4.957 7833 Z= 0.291 Chirality : 0.039 0.155 898 Planarity : 0.005 0.045 775 Dihedral : 22.656 179.091 1449 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.60 % Allowed : 25.77 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.40), residues: 492 helix: 2.14 (0.35), residues: 215 sheet: -1.48 (0.60), residues: 70 loop : -0.55 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 552 HIS 0.001 0.001 HIS A 121 PHE 0.010 0.001 PHE A 350 TYR 0.016 0.002 TYR A 432 ARG 0.005 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.480 Fit side-chains REVERT: A 365 THR cc_start: 0.7877 (p) cc_final: 0.7665 (t) REVERT: A 372 GLU cc_start: 0.8465 (tp30) cc_final: 0.8172 (tp30) REVERT: A 544 ARG cc_start: 0.7421 (tpt170) cc_final: 0.6817 (tpp-160) REVERT: A 549 ASP cc_start: 0.7783 (m-30) cc_final: 0.7353 (m-30) outliers start: 11 outliers final: 9 residues processed: 42 average time/residue: 0.2649 time to fit residues: 13.7218 Evaluate side-chains 43 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.168445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125094 restraints weight = 7038.993| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.93 r_work: 0.3335 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5569 Z= 0.163 Angle : 0.510 5.054 7833 Z= 0.269 Chirality : 0.037 0.164 898 Planarity : 0.005 0.045 775 Dihedral : 22.493 178.260 1449 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.13 % Allowed : 25.77 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.40), residues: 492 helix: 2.29 (0.36), residues: 215 sheet: -1.34 (0.61), residues: 69 loop : -0.52 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 318 HIS 0.001 0.000 HIS A 383 PHE 0.008 0.001 PHE A 137 TYR 0.017 0.001 TYR A 432 ARG 0.006 0.000 ARG A 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.547 Fit side-chains REVERT: A 365 THR cc_start: 0.7834 (p) cc_final: 0.7604 (t) REVERT: A 372 GLU cc_start: 0.8527 (tp30) cc_final: 0.8218 (tp30) REVERT: A 544 ARG cc_start: 0.7341 (tpt170) cc_final: 0.6763 (tpp-160) REVERT: A 549 ASP cc_start: 0.7735 (m-30) cc_final: 0.7305 (m-30) outliers start: 9 outliers final: 8 residues processed: 43 average time/residue: 0.2416 time to fit residues: 13.0994 Evaluate side-chains 44 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.166283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123230 restraints weight = 7061.254| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.90 r_work: 0.3314 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5569 Z= 0.218 Angle : 0.530 5.808 7833 Z= 0.279 Chirality : 0.038 0.184 898 Planarity : 0.005 0.044 775 Dihedral : 22.515 178.568 1449 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 1.65 % Allowed : 26.48 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.40), residues: 492 helix: 2.26 (0.35), residues: 215 sheet: -1.38 (0.61), residues: 69 loop : -0.52 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 552 HIS 0.001 0.000 HIS A 121 PHE 0.009 0.001 PHE A 137 TYR 0.016 0.001 TYR A 432 ARG 0.005 0.000 ARG A 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.706 Fit side-chains REVERT: A 365 THR cc_start: 0.7841 (p) cc_final: 0.7615 (t) REVERT: A 372 GLU cc_start: 0.8491 (tp30) cc_final: 0.8185 (tp30) REVERT: A 544 ARG cc_start: 0.7359 (tpt170) cc_final: 0.6791 (tpp-160) REVERT: A 549 ASP cc_start: 0.7743 (m-30) cc_final: 0.7308 (m-30) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.2589 time to fit residues: 13.4313 Evaluate side-chains 41 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 383 HIS Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 596 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 15 optimal weight: 0.0170 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.166718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123880 restraints weight = 7103.856| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.90 r_work: 0.3325 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5569 Z= 0.191 Angle : 0.524 5.503 7833 Z= 0.276 Chirality : 0.037 0.181 898 Planarity : 0.005 0.044 775 Dihedral : 22.517 178.478 1449 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 1.65 % Allowed : 26.48 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.40), residues: 492 helix: 2.28 (0.35), residues: 215 sheet: -1.36 (0.61), residues: 69 loop : -0.52 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 249 HIS 0.001 0.000 HIS A 253 PHE 0.009 0.001 PHE A 137 TYR 0.017 0.001 TYR A 432 ARG 0.006 0.000 ARG A 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3658.99 seconds wall clock time: 63 minutes 33.93 seconds (3813.93 seconds total)