Starting phenix.real_space_refine on Sun Mar 10 20:52:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eng_31210/03_2024/7eng_31210.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eng_31210/03_2024/7eng_31210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eng_31210/03_2024/7eng_31210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eng_31210/03_2024/7eng_31210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eng_31210/03_2024/7eng_31210.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eng_31210/03_2024/7eng_31210.pdb" } resolution = 3.59 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3127 2.51 5 N 826 2.21 5 O 979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ASP 1": "OD1" <-> "OD2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L GLU 61": "OE1" <-> "OE2" Residue "L ASP 66": "OD1" <-> "OD2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L ASP 88": "OD1" <-> "OD2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 114": "NH1" <-> "NH2" Residue "L PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 148": "NH1" <-> "NH2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "L TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "H GLU 101": "OE1" <-> "OE2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 158": "OE1" <-> "OE2" Residue "H PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 218": "OD1" <-> "OD2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ASP 467": "OD1" <-> "OD2" 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: 4954 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1689 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 207} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1694 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 213} Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.14, per 1000 atoms: 0.63 Number of scatterers: 4954 At special positions: 0 Unit cell: (93.7251, 87.2613, 108.807, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 979 8.00 N 826 7.00 C 3127 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.04 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 866.0 milliseconds 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1186 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 12 sheets defined 11.7% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.519A pdb=" N ASP L 88 " --> pdb=" O GLN L 85 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL L 89 " --> pdb=" O ALA L 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 85 through 89' Processing helix chain 'L' and resid 127 through 132 Processing helix chain 'L' and resid 188 through 194 removed outlier: 3.553A pdb=" N TYR L 192 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS L 194 " --> pdb=" O ALA L 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.200A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.084A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.772A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.575A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 59 through 60 removed outlier: 3.611A pdb=" N TYR L 55 " --> pdb=" O THR L 59 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 120 through 121 Processing sheet with id=AA4, first strand: chain 'L' and resid 151 through 156 removed outlier: 3.875A pdb=" N LYS L 151 " --> pdb=" O THR L 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR L 198 " --> pdb=" O PHE L 215 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL L 202 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL L 211 " --> pdb=" O VAL L 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA7, first strand: chain 'H' and resid 59 through 60 removed outlier: 4.028A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR H 112 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.323A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL H 191 " --> pdb=" O HIS H 174 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.323A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 161 through 164 removed outlier: 4.051A pdb=" N TYR H 204 " --> pdb=" O VAL H 221 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.612A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 452 through 454 158 hydrogen bonds defined for protein. 399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 805 1.31 - 1.44: 1466 1.44 - 1.57: 2781 1.57 - 1.70: 0 1.70 - 1.83: 25 Bond restraints: 5077 Sorted by residual: bond pdb=" C7 NAG A 1 " pdb=" N2 NAG A 1 " ideal model delta sigma weight residual 1.346 1.455 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C7 NAG A 2 " pdb=" N2 NAG A 2 " ideal model delta sigma weight residual 1.346 1.449 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.474 -0.061 2.00e-02 2.50e+03 9.38e+00 ... (remaining 5072 not shown) Histogram of bond angle deviations from ideal: 99.85 - 106.70: 167 106.70 - 113.55: 2722 113.55 - 120.40: 1856 120.40 - 127.26: 2115 127.26 - 134.11: 53 Bond angle restraints: 6913 Sorted by residual: angle pdb=" C SER H 140 " pdb=" N THR H 141 " pdb=" CA THR H 141 " ideal model delta sigma weight residual 122.42 112.34 10.08 1.33e+00 5.65e-01 5.75e+01 angle pdb=" N PRO H 133 " pdb=" CA PRO H 133 " pdb=" C PRO H 133 " ideal model delta sigma weight residual 111.38 117.90 -6.52 1.59e+00 3.96e-01 1.68e+01 angle pdb=" N SER H 137 " pdb=" CA SER H 137 " pdb=" C SER H 137 " ideal model delta sigma weight residual 111.28 107.11 4.17 1.09e+00 8.42e-01 1.47e+01 angle pdb=" CB GLN L 6 " pdb=" CG GLN L 6 " pdb=" CD GLN L 6 " ideal model delta sigma weight residual 112.60 106.33 6.27 1.70e+00 3.46e-01 1.36e+01 angle pdb=" N LYS H 139 " pdb=" CA LYS H 139 " pdb=" C LYS H 139 " ideal model delta sigma weight residual 113.97 109.49 4.48 1.28e+00 6.10e-01 1.22e+01 ... (remaining 6908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.72: 2840 23.72 - 47.44: 152 47.44 - 71.16: 25 71.16 - 94.88: 14 94.88 - 118.60: 8 Dihedral angle restraints: 3039 sinusoidal: 1177 harmonic: 1862 Sorted by residual: dihedral pdb=" CA PRO B 337 " pdb=" C PRO B 337 " pdb=" N PHE B 338 " pdb=" CA PHE B 338 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CB CYS L 140 " pdb=" SG CYS L 140 " pdb=" SG CYS L 200 " pdb=" CB CYS L 200 " ideal model delta sinusoidal sigma weight residual 93.00 51.38 41.62 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" CA SER L 33 " pdb=" C SER L 33 " pdb=" N ASN L 34 " pdb=" CA ASN L 34 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 3036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 710 0.092 - 0.183: 54 0.183 - 0.274: 2 0.274 - 0.366: 1 0.366 - 0.457: 1 Chirality restraints: 768 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CA LEU H 134 " pdb=" N LEU H 134 " pdb=" C LEU H 134 " pdb=" CB LEU H 134 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB THR H 100 " pdb=" CA THR H 100 " pdb=" OG1 THR H 100 " pdb=" CG2 THR H 100 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 765 not shown) Planarity restraints: 891 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE H 132 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.73e+00 pdb=" C PHE H 132 " -0.051 2.00e-02 2.50e+03 pdb=" O PHE H 132 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO H 133 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO L 49 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO L 50 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO L 50 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 50 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET L 4 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C MET L 4 " 0.026 2.00e-02 2.50e+03 pdb=" O MET L 4 " -0.010 2.00e-02 2.50e+03 pdb=" N THR L 5 " -0.009 2.00e-02 2.50e+03 ... (remaining 888 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 515 2.74 - 3.28: 4860 3.28 - 3.82: 7939 3.82 - 4.36: 9396 4.36 - 4.90: 16619 Nonbonded interactions: 39329 Sorted by model distance: nonbonded pdb=" O THR B 393 " pdb=" OG1 THR B 523 " model vdw 2.204 2.440 nonbonded pdb=" OG SER B 349 " pdb=" O LEU B 452 " model vdw 2.215 2.440 nonbonded pdb=" OG1 THR H 28 " pdb=" OG SER H 31 " model vdw 2.249 2.440 nonbonded pdb=" NE2 GLN B 474 " pdb=" O THR B 478 " model vdw 2.254 2.520 nonbonded pdb=" OG SER L 33 " pdb=" N SER B 349 " model vdw 2.255 2.520 ... (remaining 39324 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.000 Extract box with map and model: 11.410 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 18.160 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 5077 Z= 0.437 Angle : 0.825 10.081 6913 Z= 0.457 Chirality : 0.053 0.457 768 Planarity : 0.005 0.051 890 Dihedral : 17.374 118.598 1835 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.36 % Allowed : 0.91 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.69 (0.32), residues: 634 helix: -3.42 (0.70), residues: 41 sheet: -1.32 (0.31), residues: 254 loop : -1.92 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 56 HIS 0.005 0.001 HIS L 95 PHE 0.018 0.002 PHE L 215 TYR 0.022 0.002 TYR L 31 ARG 0.007 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 30 LEU cc_start: 0.8286 (tt) cc_final: 0.8060 (tp) REVERT: H 53 TYR cc_start: 0.7338 (p90) cc_final: 0.7068 (p90) REVERT: H 60 TYR cc_start: 0.8269 (m-80) cc_final: 0.7968 (m-80) REVERT: H 161 THR cc_start: 0.7024 (p) cc_final: 0.6816 (p) REVERT: B 467 ASP cc_start: 0.7461 (p0) cc_final: 0.6930 (p0) outliers start: 2 outliers final: 1 residues processed: 84 average time/residue: 0.2096 time to fit residues: 21.7849 Evaluate side-chains 65 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 0.0980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 130 GLN L 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5077 Z= 0.245 Angle : 0.653 8.485 6913 Z= 0.331 Chirality : 0.048 0.362 768 Planarity : 0.005 0.040 890 Dihedral : 12.827 90.517 742 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.73 % Allowed : 9.98 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.34 (0.32), residues: 634 helix: -3.19 (0.76), residues: 34 sheet: -1.06 (0.32), residues: 246 loop : -1.74 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.001 HIS L 204 PHE 0.014 0.002 PHE L 215 TYR 0.015 0.002 TYR L 55 ARG 0.004 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7191 (p90) cc_final: 0.6935 (p90) REVERT: H 60 TYR cc_start: 0.8210 (m-80) cc_final: 0.7995 (m-80) REVERT: B 357 ARG cc_start: 0.7513 (ttp80) cc_final: 0.7212 (mtp85) REVERT: B 383 SER cc_start: 0.8236 (t) cc_final: 0.8019 (p) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.2006 time to fit residues: 18.4915 Evaluate side-chains 63 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 164 ASN Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 5077 Z= 0.324 Angle : 0.665 7.996 6913 Z= 0.336 Chirality : 0.047 0.392 768 Planarity : 0.004 0.040 890 Dihedral : 9.559 65.907 741 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 1.63 % Allowed : 14.16 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.25 (0.32), residues: 634 helix: -3.10 (0.80), residues: 34 sheet: -0.95 (0.32), residues: 244 loop : -1.72 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.020 0.002 PHE H 156 TYR 0.023 0.002 TYR H 155 ARG 0.005 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 146 TYR cc_start: 0.8346 (t80) cc_final: 0.8113 (t80) REVERT: H 53 TYR cc_start: 0.7221 (p90) cc_final: 0.6959 (p90) REVERT: H 60 TYR cc_start: 0.8228 (m-80) cc_final: 0.7932 (m-80) REVERT: B 383 SER cc_start: 0.8299 (t) cc_final: 0.8063 (p) outliers start: 9 outliers final: 7 residues processed: 81 average time/residue: 0.1976 time to fit residues: 20.1073 Evaluate side-chains 71 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 164 ASN Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 5077 Z= 0.417 Angle : 0.706 8.061 6913 Z= 0.357 Chirality : 0.048 0.403 768 Planarity : 0.005 0.044 890 Dihedral : 7.840 43.182 741 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.09 % Allowed : 15.79 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.30 (0.32), residues: 634 helix: -3.16 (0.76), residues: 34 sheet: -0.98 (0.32), residues: 244 loop : -1.76 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.002 PHE L 124 TYR 0.020 0.002 TYR L 55 ARG 0.005 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7260 (p90) cc_final: 0.7002 (p90) REVERT: H 60 TYR cc_start: 0.8253 (m-80) cc_final: 0.7977 (m-80) REVERT: B 383 SER cc_start: 0.8326 (t) cc_final: 0.8090 (p) outliers start: 17 outliers final: 13 residues processed: 82 average time/residue: 0.1829 time to fit residues: 19.0138 Evaluate side-chains 76 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 164 ASN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5077 Z= 0.245 Angle : 0.635 8.522 6913 Z= 0.317 Chirality : 0.046 0.396 768 Planarity : 0.004 0.038 890 Dihedral : 7.019 42.833 741 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.36 % Allowed : 18.87 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.26 (0.32), residues: 634 helix: -3.18 (0.67), residues: 40 sheet: -0.91 (0.32), residues: 242 loop : -1.72 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.023 0.001 PHE H 156 TYR 0.018 0.002 TYR H 155 ARG 0.006 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7188 (p90) cc_final: 0.6968 (p90) REVERT: H 173 VAL cc_start: 0.8223 (t) cc_final: 0.7979 (m) REVERT: B 383 SER cc_start: 0.8315 (t) cc_final: 0.8069 (p) outliers start: 13 outliers final: 12 residues processed: 78 average time/residue: 0.2031 time to fit residues: 20.2028 Evaluate side-chains 74 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 164 ASN Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5077 Z= 0.347 Angle : 0.656 7.844 6913 Z= 0.331 Chirality : 0.046 0.362 768 Planarity : 0.004 0.040 890 Dihedral : 6.744 41.496 741 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.90 % Allowed : 19.06 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.25 (0.32), residues: 634 helix: -3.10 (0.70), residues: 40 sheet: -0.91 (0.33), residues: 242 loop : -1.72 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.010 0.001 PHE L 124 TYR 0.017 0.002 TYR L 55 ARG 0.005 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7158 (p90) cc_final: 0.6927 (p90) REVERT: H 173 VAL cc_start: 0.8236 (t) cc_final: 0.7993 (m) REVERT: B 383 SER cc_start: 0.8337 (t) cc_final: 0.8076 (p) outliers start: 16 outliers final: 12 residues processed: 76 average time/residue: 0.1865 time to fit residues: 18.1215 Evaluate side-chains 70 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 164 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 50 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5077 Z= 0.294 Angle : 0.641 7.618 6913 Z= 0.324 Chirality : 0.047 0.361 768 Planarity : 0.004 0.038 890 Dihedral : 6.490 42.037 741 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.45 % Allowed : 18.87 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.19 (0.32), residues: 634 helix: -2.98 (0.72), residues: 40 sheet: -0.82 (0.33), residues: 237 loop : -1.72 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 56 HIS 0.005 0.001 HIS H 35 PHE 0.026 0.002 PHE H 156 TYR 0.017 0.002 TYR L 55 ARG 0.006 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 53 TYR cc_start: 0.7065 (p90) cc_final: 0.6863 (p90) REVERT: H 173 VAL cc_start: 0.8209 (t) cc_final: 0.7929 (m) REVERT: B 383 SER cc_start: 0.8340 (t) cc_final: 0.8069 (p) REVERT: B 408 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6595 (ptm160) outliers start: 19 outliers final: 15 residues processed: 77 average time/residue: 0.1788 time to fit residues: 17.6195 Evaluate side-chains 76 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 164 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 8.9990 chunk 40 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 5077 Z= 0.299 Angle : 0.633 7.643 6913 Z= 0.321 Chirality : 0.046 0.345 768 Planarity : 0.004 0.039 890 Dihedral : 6.248 42.283 741 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.09 % Allowed : 19.42 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.20 (0.32), residues: 634 helix: -2.95 (0.71), residues: 40 sheet: -0.83 (0.33), residues: 237 loop : -1.74 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 436 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.001 PHE L 124 TYR 0.016 0.002 TYR H 155 ARG 0.007 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 173 VAL cc_start: 0.8251 (t) cc_final: 0.7961 (m) REVERT: B 383 SER cc_start: 0.8341 (t) cc_final: 0.8062 (p) REVERT: B 408 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.6570 (ptm160) outliers start: 17 outliers final: 15 residues processed: 76 average time/residue: 0.1985 time to fit residues: 19.1091 Evaluate side-chains 76 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 164 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5077 Z= 0.269 Angle : 0.621 7.567 6913 Z= 0.314 Chirality : 0.046 0.346 768 Planarity : 0.004 0.038 890 Dihedral : 6.065 43.784 741 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.09 % Allowed : 19.60 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.32), residues: 634 helix: -2.84 (0.74), residues: 40 sheet: -0.78 (0.33), residues: 237 loop : -1.72 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.027 0.002 PHE H 156 TYR 0.017 0.002 TYR H 155 ARG 0.005 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 173 VAL cc_start: 0.8244 (t) cc_final: 0.7974 (m) REVERT: B 383 SER cc_start: 0.8347 (t) cc_final: 0.8059 (p) REVERT: B 408 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.6605 (ptm160) outliers start: 17 outliers final: 15 residues processed: 74 average time/residue: 0.1970 time to fit residues: 18.5728 Evaluate side-chains 76 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 164 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5077 Z= 0.207 Angle : 0.592 7.200 6913 Z= 0.299 Chirality : 0.045 0.293 768 Planarity : 0.004 0.036 890 Dihedral : 5.798 46.992 741 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.09 % Allowed : 19.78 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.04 (0.32), residues: 634 helix: -2.88 (0.70), residues: 41 sheet: -0.70 (0.32), residues: 238 loop : -1.64 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS H 35 PHE 0.027 0.001 PHE H 156 TYR 0.019 0.001 TYR B 396 ARG 0.002 0.000 ARG B 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 27 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: H 173 VAL cc_start: 0.8166 (t) cc_final: 0.7894 (m) REVERT: B 383 SER cc_start: 0.8377 (t) cc_final: 0.8091 (p) outliers start: 17 outliers final: 15 residues processed: 76 average time/residue: 0.1715 time to fit residues: 16.9740 Evaluate side-chains 77 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain L residue 164 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 0.0970 chunk 20 optimal weight: 6.9990 chunk 50 optimal weight: 0.0170 chunk 6 optimal weight: 0.0870 chunk 9 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.217232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.185676 restraints weight = 6028.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.184389 restraints weight = 11364.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.186187 restraints weight = 9717.583| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5077 Z= 0.157 Angle : 0.584 8.315 6913 Z= 0.295 Chirality : 0.044 0.264 768 Planarity : 0.004 0.034 890 Dihedral : 5.645 53.376 741 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.90 % Allowed : 20.33 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 (0.32), residues: 634 helix: -2.64 (0.74), residues: 41 sheet: -0.54 (0.33), residues: 235 loop : -1.60 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS H 35 PHE 0.011 0.001 PHE L 145 TYR 0.022 0.001 TYR B 396 ARG 0.005 0.000 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1408.47 seconds wall clock time: 26 minutes 18.29 seconds (1578.29 seconds total)