Starting phenix.real_space_refine on Fri Mar 15 06:41:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnp_33322/03_2024/7xnp_33322.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnp_33322/03_2024/7xnp_33322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnp_33322/03_2024/7xnp_33322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnp_33322/03_2024/7xnp_33322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnp_33322/03_2024/7xnp_33322.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnp_33322/03_2024/7xnp_33322.pdb" } resolution = 2.9 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= 0.008 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 245 5.49 5 S 12 5.16 5 C 6107 2.51 5 N 2058 2.21 5 O 2521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 68": "OD1" <-> "OD2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "F TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10943 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 750 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2535 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "J" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2505 Classifications: {'DNA': 123} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 122} Time building chain proxies: 6.30, per 1000 atoms: 0.58 Number of scatterers: 10943 At special positions: 0 Unit cell: (97.836, 123.084, 109.408, 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 12 16.00 P 245 15.00 O 2521 8.00 N 2058 7.00 C 6107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 9 sheets defined 72.0% alpha, 2.9% beta 123 base pairs and 227 stacking pairs defined. Time for finding SS restraints: 5.41 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.580A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.804A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.570A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.437A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.517A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.504A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.653A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.814A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.624A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.302A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.550A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.627A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.522A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.098A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.216A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.869A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.938A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 395 hydrogen bonds defined for protein. 1173 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 318 hydrogen bonds 632 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 227 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 5.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2006 1.33 - 1.45: 3792 1.45 - 1.57: 5324 1.57 - 1.69: 489 1.69 - 1.81: 22 Bond restraints: 11633 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.480 -0.058 3.00e-02 1.11e+03 3.77e+00 bond pdb=" C3' DG I 4 " pdb=" O3' DG I 4 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.39e+00 bond pdb=" C3' DC J 21 " pdb=" O3' DC J 21 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.82e+00 bond pdb=" C LEU E 65 " pdb=" N PRO E 66 " ideal model delta sigma weight residual 1.335 1.355 -0.019 1.36e-02 5.41e+03 2.04e+00 bond pdb=" CB THR H 93 " pdb=" CG2 THR H 93 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 ... (remaining 11628 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.27: 1101 105.27 - 112.34: 6350 112.34 - 119.40: 3668 119.40 - 126.46: 4909 126.46 - 133.53: 734 Bond angle restraints: 16762 Sorted by residual: angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 121.70 -8.52 2.37e+00 1.78e-01 1.29e+01 angle pdb=" N GLU H 110 " pdb=" CA GLU H 110 " pdb=" CB GLU H 110 " ideal model delta sigma weight residual 110.40 116.03 -5.63 1.63e+00 3.76e-01 1.19e+01 angle pdb=" C3' DG I 4 " pdb=" O3' DG I 4 " pdb=" P DT I 5 " ideal model delta sigma weight residual 120.20 124.96 -4.76 1.50e+00 4.44e-01 1.01e+01 angle pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sigma weight residual 120.20 124.87 -4.67 1.50e+00 4.44e-01 9.69e+00 angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 113.18 120.44 -7.26 2.37e+00 1.78e-01 9.38e+00 ... (remaining 16757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 5149 35.05 - 70.10: 1191 70.10 - 105.15: 17 105.15 - 140.20: 1 140.20 - 175.25: 2 Dihedral angle restraints: 6360 sinusoidal: 4201 harmonic: 2159 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -159.08 -20.92 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 35.25 -175.25 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC J 21 " pdb=" C3' DC J 21 " pdb=" O3' DC J 21 " pdb=" P DC J 22 " ideal model delta sinusoidal sigma weight residual 220.00 72.16 147.84 1 3.50e+01 8.16e-04 1.45e+01 ... (remaining 6357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1503 0.051 - 0.101: 337 0.101 - 0.152: 64 0.152 - 0.203: 7 0.203 - 0.254: 2 Chirality restraints: 1913 Sorted by residual: chirality pdb=" CA GLU H 110 " pdb=" N GLU H 110 " pdb=" C GLU H 110 " pdb=" CB GLU H 110 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" P DC J 22 " pdb=" OP1 DC J 22 " pdb=" OP2 DC J 22 " pdb=" O5' DC J 22 " both_signs ideal model delta sigma weight residual True 2.35 -2.56 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL D 108 " pdb=" CA VAL D 108 " pdb=" CG1 VAL D 108 " pdb=" CG2 VAL D 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 1910 not shown) Planarity restraints: 1271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO C 80 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO G 80 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -26 " 0.031 2.00e-02 2.50e+03 1.60e-02 5.75e+00 pdb=" N1 DC I -26 " -0.032 2.00e-02 2.50e+03 pdb=" C2 DC I -26 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC I -26 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC I -26 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DC I -26 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC I -26 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DC I -26 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC I -26 " -0.003 2.00e-02 2.50e+03 ... (remaining 1268 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2503 2.82 - 3.34: 8917 3.34 - 3.86: 21917 3.86 - 4.38: 25725 4.38 - 4.90: 36485 Nonbonded interactions: 95547 Sorted by model distance: nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.297 2.440 nonbonded pdb=" N2 DG I -21 " pdb=" O2 DC J 21 " model vdw 2.326 2.496 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.371 2.440 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.376 2.440 nonbonded pdb=" NH2 ARG C 88 " pdb=" O VAL C 100 " model vdw 2.387 2.520 ... (remaining 95542 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 43 through 133) selection = (chain 'E' and resid 43 through 133) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.550 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: 2.250 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 36.800 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 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 0.058 11633 Z= 0.273 Angle : 0.748 8.527 16762 Z= 0.442 Chirality : 0.045 0.254 1913 Planarity : 0.006 0.070 1271 Dihedral : 27.194 175.251 4968 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.27), residues: 730 helix: -0.52 (0.19), residues: 534 sheet: None (None), residues: 0 loop : -0.46 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 75 PHE 0.014 0.002 PHE H 67 TYR 0.019 0.002 TYR B 88 ARG 0.008 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.840 Fit side-chains REVERT: A 118 THR cc_start: 0.8782 (m) cc_final: 0.8542 (m) REVERT: C 95 LYS cc_start: 0.7302 (mmpt) cc_final: 0.7097 (mtmt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 1.8270 time to fit residues: 203.8750 Evaluate side-chains 91 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 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 76 GLN B 93 GLN C 89 ASN G 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11633 Z= 0.186 Angle : 0.557 7.594 16762 Z= 0.337 Chirality : 0.035 0.140 1913 Planarity : 0.004 0.051 1271 Dihedral : 30.352 175.114 3504 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.62 % Allowed : 7.43 % Favored : 90.95 % 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: 1.15 (0.29), residues: 730 helix: 1.19 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -0.29 (0.40), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.009 0.002 PHE A 67 TYR 0.015 0.001 TYR G 57 ARG 0.007 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 0.829 Fit side-chains REVERT: E 64 LYS cc_start: 0.8107 (mptm) cc_final: 0.7838 (mptt) REVERT: F 91 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7537 (ttpp) outliers start: 10 outliers final: 5 residues processed: 101 average time/residue: 1.7209 time to fit residues: 183.6823 Evaluate side-chains 100 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 44 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 89 ASN D 92 GLN D 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11633 Z= 0.321 Angle : 0.635 8.387 16762 Z= 0.375 Chirality : 0.040 0.147 1913 Planarity : 0.005 0.048 1271 Dihedral : 30.698 172.304 3504 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.39 % Allowed : 9.53 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 730 helix: 1.43 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.34 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 46 PHE 0.014 0.002 PHE H 67 TYR 0.014 0.002 TYR G 57 ARG 0.005 0.001 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: C 77 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.7089 (tpt-90) REVERT: C 95 LYS cc_start: 0.7531 (mmpt) cc_final: 0.7118 (mtmt) REVERT: E 64 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7847 (mptt) outliers start: 21 outliers final: 9 residues processed: 111 average time/residue: 1.7512 time to fit residues: 204.8424 Evaluate side-chains 108 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 44 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11633 Z= 0.236 Angle : 0.601 8.298 16762 Z= 0.361 Chirality : 0.037 0.139 1913 Planarity : 0.004 0.046 1271 Dihedral : 30.693 172.817 3504 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.75 % Allowed : 11.63 % Favored : 85.62 % 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: 1.73 (0.29), residues: 730 helix: 1.69 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.36 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 106 PHE 0.013 0.002 PHE F 61 TYR 0.016 0.002 TYR G 57 ARG 0.005 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: C 77 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.7031 (tpt-90) REVERT: C 95 LYS cc_start: 0.7580 (mmpt) cc_final: 0.7098 (mtmt) REVERT: D 68 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6551 (pt0) REVERT: E 64 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7817 (mptt) REVERT: E 120 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7021 (mtt) REVERT: F 91 LYS cc_start: 0.8033 (ttpt) cc_final: 0.7787 (ttmt) outliers start: 17 outliers final: 11 residues processed: 105 average time/residue: 1.7984 time to fit residues: 199.6137 Evaluate side-chains 110 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11633 Z= 0.205 Angle : 0.587 8.214 16762 Z= 0.354 Chirality : 0.036 0.141 1913 Planarity : 0.004 0.045 1271 Dihedral : 30.680 172.803 3504 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.75 % Allowed : 12.44 % Favored : 84.81 % 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: 1.88 (0.29), residues: 730 helix: 1.80 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.31 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 106 PHE 0.012 0.002 PHE F 61 TYR 0.016 0.001 TYR G 57 ARG 0.016 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7650 (mmpt) cc_final: 0.7106 (mtmt) REVERT: D 68 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6358 (pt0) REVERT: E 64 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7804 (mptt) REVERT: E 120 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7015 (mtt) REVERT: F 91 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7680 (ttmm) outliers start: 17 outliers final: 11 residues processed: 102 average time/residue: 1.7139 time to fit residues: 184.8615 Evaluate side-chains 108 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 0.0670 chunk 92 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11633 Z= 0.225 Angle : 0.584 8.337 16762 Z= 0.352 Chirality : 0.037 0.143 1913 Planarity : 0.004 0.045 1271 Dihedral : 30.658 172.667 3504 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.58 % Allowed : 12.60 % Favored : 84.81 % 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: 1.96 (0.29), residues: 730 helix: 1.89 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.39 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 106 PHE 0.012 0.002 PHE F 61 TYR 0.014 0.001 TYR G 57 ARG 0.003 0.000 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.772 Fit side-chains REVERT: C 77 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.7004 (tpt-90) REVERT: C 95 LYS cc_start: 0.7543 (mmpt) cc_final: 0.7249 (mmpt) REVERT: D 57 SER cc_start: 0.7807 (m) cc_final: 0.7533 (m) REVERT: E 64 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7792 (mptt) REVERT: E 120 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.6982 (mtt) REVERT: F 91 LYS cc_start: 0.8058 (ttpt) cc_final: 0.7684 (ttmm) REVERT: G 64 GLU cc_start: 0.6896 (tp30) cc_final: 0.6668 (tp30) outliers start: 16 outliers final: 9 residues processed: 109 average time/residue: 1.7506 time to fit residues: 201.2975 Evaluate side-chains 110 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11633 Z= 0.198 Angle : 0.576 7.953 16762 Z= 0.349 Chirality : 0.036 0.143 1913 Planarity : 0.004 0.044 1271 Dihedral : 30.654 172.819 3504 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.75 % Allowed : 12.60 % Favored : 84.65 % 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: 2.03 (0.29), residues: 730 helix: 1.95 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.38 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 106 PHE 0.012 0.002 PHE F 61 TYR 0.016 0.001 TYR G 57 ARG 0.014 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: C 77 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.7052 (tpt-90) REVERT: C 95 LYS cc_start: 0.7520 (mmpt) cc_final: 0.7197 (mmpt) REVERT: D 57 SER cc_start: 0.7798 (m) cc_final: 0.7525 (m) REVERT: E 64 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7783 (mptt) REVERT: E 120 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6970 (mtt) REVERT: F 91 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7686 (ttmm) outliers start: 17 outliers final: 12 residues processed: 105 average time/residue: 1.7577 time to fit residues: 194.9656 Evaluate side-chains 112 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.0770 chunk 58 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11633 Z= 0.175 Angle : 0.569 8.404 16762 Z= 0.346 Chirality : 0.035 0.140 1913 Planarity : 0.004 0.043 1271 Dihedral : 30.645 172.900 3504 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.10 % Allowed : 13.25 % Favored : 84.65 % 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: 2.12 (0.30), residues: 730 helix: 2.00 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.33 (0.40), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.011 0.001 PHE F 61 TYR 0.016 0.001 TYR G 57 ARG 0.006 0.000 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.746 Fit side-chains REVERT: C 77 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.7026 (tpt-90) REVERT: C 95 LYS cc_start: 0.7523 (mmpt) cc_final: 0.7194 (mmpt) REVERT: D 57 SER cc_start: 0.7788 (m) cc_final: 0.7515 (m) REVERT: E 64 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7790 (mptt) REVERT: E 120 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.6949 (mtt) REVERT: F 91 LYS cc_start: 0.8051 (ttpt) cc_final: 0.7682 (ttmm) outliers start: 13 outliers final: 8 residues processed: 103 average time/residue: 1.7099 time to fit residues: 185.8006 Evaluate side-chains 107 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 0.0010 chunk 77 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 76 GLN C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11633 Z= 0.302 Angle : 0.619 8.679 16762 Z= 0.368 Chirality : 0.039 0.148 1913 Planarity : 0.005 0.043 1271 Dihedral : 30.675 173.891 3504 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.75 % Allowed : 12.60 % Favored : 84.65 % 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: 1.86 (0.29), residues: 730 helix: 1.80 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.37 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 106 PHE 0.014 0.002 PHE F 61 TYR 0.015 0.002 TYR G 57 ARG 0.009 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.7546 (mmpt) cc_final: 0.7079 (mtmt) REVERT: E 64 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7865 (mptt) REVERT: F 91 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7912 (ttmm) REVERT: F 92 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6950 (ttp80) outliers start: 17 outliers final: 11 residues processed: 111 average time/residue: 1.7441 time to fit residues: 204.1768 Evaluate side-chains 110 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11633 Z= 0.238 Angle : 0.606 8.602 16762 Z= 0.363 Chirality : 0.037 0.146 1913 Planarity : 0.005 0.043 1271 Dihedral : 30.674 173.907 3504 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.42 % Allowed : 13.25 % Favored : 84.33 % 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: 1.90 (0.29), residues: 730 helix: 1.83 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.38 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 106 PHE 0.013 0.002 PHE F 61 TYR 0.017 0.002 TYR G 57 ARG 0.009 0.000 ARG H 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7263 (tt0) REVERT: C 95 LYS cc_start: 0.7545 (mmpt) cc_final: 0.7068 (mtmt) REVERT: E 64 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7851 (mptt) REVERT: F 91 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7920 (ttmm) outliers start: 15 outliers final: 11 residues processed: 107 average time/residue: 1.7216 time to fit residues: 194.3685 Evaluate side-chains 109 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 32 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 89 ASN D 92 GLN E 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.188582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.156738 restraints weight = 10343.902| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 0.60 r_work: 0.3543 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11633 Z= 0.187 Angle : 0.591 7.579 16762 Z= 0.357 Chirality : 0.036 0.140 1913 Planarity : 0.004 0.043 1271 Dihedral : 30.672 173.875 3504 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.75 % Allowed : 12.92 % Favored : 84.33 % 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: 2.03 (0.30), residues: 730 helix: 1.94 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.41 (0.40), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 106 PHE 0.013 0.002 PHE F 61 TYR 0.019 0.001 TYR G 57 ARG 0.008 0.000 ARG H 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3461.20 seconds wall clock time: 61 minutes 37.09 seconds (3697.09 seconds total)