Starting phenix.real_space_refine on Fri Sep 11 08:07:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y5w_33627/09_2026/7y5w_33627.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5w_33627/09_2026/7y5w_33627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y5w_33627/09_2026/7y5w_33627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5w_33627/09_2026/7y5w_33627.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y5w_33627/09_2026/7y5w_33627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5w_33627/09_2026/7y5w_33627.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.017 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 202 5.49 5 S 20 5.16 5 C 4911 2.51 5 N 1652 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8811 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "B" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 561 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "C" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 608 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "D" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "E" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 615 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "G" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 591 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "H" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 524 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "I" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2054 Classifications: {'DNA': 101} Link IDs: {'rna3p': 100} Chain: "J" Number of atoms: 2087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 2087 Classifications: {'DNA': 101} Link IDs: {'rna3p': 100} Time building chain proxies: 1.79, per 1000 atoms: 0.20 Number of scatterers: 8811 At special positions: 0 Unit cell: (82, 114, 116, 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 20 16.00 P 202 15.00 O 2026 8.00 N 1652 7.00 C 4911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 212.9 milliseconds 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1100 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 5 sheets defined 79.1% alpha, 1.7% beta 90 base pairs and 167 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.505A 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: 3.653A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.501A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 85 through 114 Processing helix chain 'C' and resid 120 through 131 Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 47 through 76 removed outlier: 4.209A pdb=" N TYR D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU D 52 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.503A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.548A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 79 removed outlier: 3.561A pdb=" N PHE G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 Processing helix chain 'G' and resid 120 through 132 removed outlier: 3.803A pdb=" N ILE G 124 " --> pdb=" O MET G 120 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 77 Processing helix chain 'H' and resid 82 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 84 removed outlier: 7.247A pdb=" N ARG C 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.326A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 349 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 231 hydrogen bonds 442 hydrogen bond angles 0 basepair planarities 90 basepair parallelities 167 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1879 1.34 - 1.45: 2816 1.45 - 1.57: 4233 1.57 - 1.69: 402 1.69 - 1.81: 32 Bond restraints: 9362 Sorted by residual: bond pdb=" C3' DA I 103 " pdb=" C2' DA I 103 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DG I 85 " pdb=" C2' DG I 85 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.80e+00 bond pdb=" C3' DC I 64 " pdb=" C2' DC I 64 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.32e+00 bond pdb=" C3' DG I 63 " pdb=" C2' DG I 63 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.22e+00 bond pdb=" C3' DG I 76 " pdb=" C2' DG I 76 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.21e+00 ... (remaining 9357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 12917 1.80 - 3.61: 547 3.61 - 5.41: 23 5.41 - 7.22: 0 7.22 - 9.02: 1 Bond angle restraints: 13488 Sorted by residual: angle pdb=" O4' DG I 121 " pdb=" C4' DG I 121 " pdb=" C3' DG I 121 " ideal model delta sigma weight residual 106.00 103.04 2.96 6.00e-01 2.78e+00 2.43e+01 angle pdb=" O4' DG I 101 " pdb=" C4' DG I 101 " pdb=" C3' DG I 101 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT I 104 " pdb=" C4 DT I 104 " pdb=" O4 DT I 104 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" O4' DA I 60 " pdb=" C4' DA I 60 " pdb=" C3' DA I 60 " ideal model delta sigma weight residual 106.00 103.37 2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" O4' DT I 105 " pdb=" C1' DT I 105 " pdb=" N1 DT I 105 " ideal model delta sigma weight residual 108.00 111.06 -3.06 7.00e-01 2.04e+00 1.91e+01 ... (remaining 13483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.06: 3940 29.06 - 58.13: 1086 58.13 - 87.19: 104 87.19 - 116.25: 1 116.25 - 145.31: 4 Dihedral angle restraints: 5135 sinusoidal: 3448 harmonic: 1687 Sorted by residual: dihedral pdb=" C4' DG I 73 " pdb=" C3' DG I 73 " pdb=" O3' DG I 73 " pdb=" P DC I 74 " ideal model delta sinusoidal sigma weight residual 220.00 74.69 145.31 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" C4' DT J 105 " pdb=" C3' DT J 105 " pdb=" O3' DT J 105 " pdb=" P DG J 106 " ideal model delta sinusoidal sigma weight residual 220.00 89.58 130.42 1 3.50e+01 8.16e-04 1.29e+01 dihedral pdb=" C4' DG I 34 " pdb=" C3' DG I 34 " pdb=" O3' DG I 34 " pdb=" P DT I 35 " ideal model delta sinusoidal sigma weight residual 220.00 91.20 128.80 1 3.50e+01 8.16e-04 1.27e+01 ... (remaining 5132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 837 0.029 - 0.059: 464 0.059 - 0.088: 168 0.088 - 0.118: 72 0.118 - 0.147: 8 Chirality restraints: 1549 Sorted by residual: chirality pdb=" C3' DG I 73 " pdb=" C4' DG I 73 " pdb=" O3' DG I 73 " pdb=" C2' DG I 73 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ILE D 29 " pdb=" N ILE D 29 " pdb=" C ILE D 29 " pdb=" CB ILE D 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" C3' DA J 40 " pdb=" C4' DA J 40 " pdb=" O3' DA J 40 " pdb=" C2' DA J 40 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 1546 not shown) Planarity restraints: 1004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET G 120 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO G 121 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO G 121 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 121 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " -0.023 2.00e-02 2.50e+03 1.04e-02 3.24e+00 pdb=" N9 DG I 121 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 110 " -0.020 2.00e-02 2.50e+03 9.51e-03 2.04e+00 pdb=" N1 DC I 110 " 0.016 2.00e-02 2.50e+03 pdb=" C2 DC I 110 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 110 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DC I 110 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC I 110 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 110 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 110 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 110 " 0.004 2.00e-02 2.50e+03 ... (remaining 1001 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 219 2.66 - 3.22: 7704 3.22 - 3.78: 17065 3.78 - 4.34: 20536 4.34 - 4.90: 29648 Nonbonded interactions: 75172 Sorted by model distance: nonbonded pdb=" N2 DG I 34 " pdb=" O2 DC J 114 " model vdw 2.102 2.496 nonbonded pdb=" N2 DG I 33 " pdb=" O2 DC J 115 " model vdw 2.118 2.496 nonbonded pdb=" N2 DG I 85 " pdb=" O2 DC J 63 " model vdw 2.139 2.496 nonbonded pdb=" O2 DC I 82 " pdb=" N2 DG J 66 " model vdw 2.156 2.496 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.228 3.040 ... (remaining 75167 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 61 through 133) selection = (chain 'C' and resid 61 through 133) selection = (chain 'E' and resid 61 through 133) selection = chain 'G' } ncs_group { reference = (chain 'B' and resid 29 through 93) selection = (chain 'D' and resid 29 through 93) selection = (chain 'F' and resid 29 through 93) 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 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: 1.200 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.570 Find NCS groups from input model: 0.070 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 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 0.040 9362 Z= 0.491 Angle : 0.711 9.023 13488 Z= 0.637 Chirality : 0.043 0.147 1549 Planarity : 0.003 0.045 1004 Dihedral : 27.557 145.314 4035 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.34), residues: 563 helix: 2.20 (0.23), residues: 458 sheet: None (None), residues: 0 loop : -0.72 (0.50), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 129 TYR 0.008 0.001 TYR B 51 PHE 0.007 0.001 PHE E 67 HIS 0.003 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.49 ( 9362) covalent geometry : angle 0.71139 / 0.64 (13488) hydrogen bonds : bond 0.09757 / 6.46 ( 580) hydrogen bonds : angle 3.60096 / 2.58 ( 1477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 ASP cc_start: 0.6597 (t70) cc_final: 0.6277 (t0) REVERT: E 60 LEU cc_start: 0.7307 (mt) cc_final: 0.6979 (mt) REVERT: E 64 LYS cc_start: 0.7126 (mptt) cc_final: 0.6879 (mttm) REVERT: F 80 THR cc_start: 0.8225 (m) cc_final: 0.7986 (p) REVERT: G 89 VAL cc_start: 0.8828 (m) cc_final: 0.8531 (m) REVERT: G 90 MET cc_start: 0.7212 (tmm) cc_final: 0.6297 (tmm) REVERT: H 60 VAL cc_start: 0.8165 (t) cc_final: 0.7947 (p) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.1203 time to fit residues: 48.7871 Evaluate side-chains 226 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.0980 chunk 61 optimal weight: 10.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 overall best weight: 3.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 93 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 HIS E 76 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.057364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.040802 restraints weight = 56932.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.042085 restraints weight = 27895.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.042895 restraints weight = 18578.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.043331 restraints weight = 14709.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.043647 restraints weight = 12973.345| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 9362 Z= 0.284 Angle : 0.805 13.300 13488 Z= 0.453 Chirality : 0.047 0.263 1549 Planarity : 0.007 0.065 1004 Dihedral : 30.855 144.855 2840 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 23.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.67 % Allowed : 28.74 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.34), residues: 563 helix: 1.64 (0.23), residues: 464 sheet: None (None), residues: 0 loop : -0.93 (0.54), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 67 TYR 0.016 0.002 TYR H 88 PHE 0.020 0.002 PHE C 78 HIS 0.007 0.002 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.28 ( 9362) covalent geometry : angle 0.80484 / 0.45 (13488) hydrogen bonds : bond 0.07256 / 4.79 ( 580) hydrogen bonds : angle 3.69845 / 2.71 ( 1477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 251 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8643 (mtm) cc_final: 0.8212 (mtm) REVERT: A 134 ARG cc_start: 0.8773 (tpp-160) cc_final: 0.8315 (tpp-160) REVERT: B 63 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9055 (mm-30) REVERT: B 68 ASP cc_start: 0.8751 (t70) cc_final: 0.8409 (t0) REVERT: B 92 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8210 (ttp80) REVERT: C 60 LEU cc_start: 0.9070 (mm) cc_final: 0.8552 (mm) REVERT: C 73 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8572 (tm-30) REVERT: C 77 ASP cc_start: 0.8957 (t70) cc_final: 0.8646 (t0) REVERT: C 97 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8002 (mt-10) REVERT: E 85 GLN cc_start: 0.9404 (OUTLIER) cc_final: 0.9170 (tt0) REVERT: E 120 MET cc_start: 0.8077 (mmm) cc_final: 0.7869 (mmm) REVERT: E 129 ARG cc_start: 0.8799 (mmm160) cc_final: 0.8246 (mmm160) REVERT: F 44 LYS cc_start: 0.9536 (OUTLIER) cc_final: 0.9232 (mmmt) REVERT: F 79 LYS cc_start: 0.9208 (mmmt) cc_final: 0.8809 (mtpp) REVERT: F 80 THR cc_start: 0.9367 (m) cc_final: 0.8871 (p) REVERT: F 88 TYR cc_start: 0.9071 (m-80) cc_final: 0.8863 (m-10) REVERT: G 120 MET cc_start: 0.8476 (mmm) cc_final: 0.8206 (mmm) REVERT: G 131 ARG cc_start: 0.8805 (mtp85) cc_final: 0.8534 (mtp85) REVERT: H 43 VAL cc_start: 0.8170 (t) cc_final: 0.7927 (t) REVERT: H 49 LEU cc_start: 0.8127 (mp) cc_final: 0.7862 (mm) REVERT: H 53 GLU cc_start: 0.9338 (mt-10) cc_final: 0.9083 (mt-10) outliers start: 28 outliers final: 21 residues processed: 259 average time/residue: 0.1102 time to fit residues: 36.6417 Evaluate side-chains 247 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain H residue 59 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 73 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 55 optimal weight: 30.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.058974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.042095 restraints weight = 52959.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.043380 restraints weight = 26238.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.044195 restraints weight = 17660.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.044680 restraints weight = 14023.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.044835 restraints weight = 12320.429| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9362 Z= 0.177 Angle : 0.727 9.869 13488 Z= 0.413 Chirality : 0.044 0.301 1549 Planarity : 0.005 0.049 1004 Dihedral : 30.990 146.117 2840 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.26 % Allowed : 28.34 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.33), residues: 563 helix: 1.44 (0.23), residues: 464 sheet: None (None), residues: 0 loop : -1.02 (0.52), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG H 36 TYR 0.016 0.002 TYR E 99 PHE 0.024 0.002 PHE A 78 HIS 0.005 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.18 ( 9362) covalent geometry : angle 0.72735 / 0.41 (13488) hydrogen bonds : bond 0.06171 / 4.06 ( 580) hydrogen bonds : angle 3.49662 / 2.56 ( 1477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 260 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8365 (mt) cc_final: 0.7967 (mp) REVERT: A 90 MET cc_start: 0.8735 (tmm) cc_final: 0.8425 (tmm) REVERT: A 112 ILE cc_start: 0.9707 (tp) cc_final: 0.9415 (pt) REVERT: B 63 GLU cc_start: 0.9321 (mt-10) cc_final: 0.8986 (mm-30) REVERT: B 67 ARG cc_start: 0.9086 (ttm-80) cc_final: 0.8879 (ttm-80) REVERT: B 68 ASP cc_start: 0.8682 (t70) cc_final: 0.8330 (t0) REVERT: B 77 LYS cc_start: 0.8288 (mttp) cc_final: 0.8023 (mmtm) REVERT: C 60 LEU cc_start: 0.9036 (mm) cc_final: 0.8446 (mm) REVERT: C 68 GLN cc_start: 0.9515 (mt0) cc_final: 0.9282 (tt0) REVERT: C 73 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8667 (tm-30) REVERT: C 77 ASP cc_start: 0.9004 (t70) cc_final: 0.8688 (t0) REVERT: C 85 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.8805 (mt0) REVERT: C 97 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7926 (mt-10) REVERT: C 105 GLU cc_start: 0.8933 (tp30) cc_final: 0.8690 (mm-30) REVERT: C 128 ARG cc_start: 0.9464 (mtp85) cc_final: 0.9203 (mtp85) REVERT: C 129 ARG cc_start: 0.9265 (tpp80) cc_final: 0.8856 (tpp80) REVERT: D 79 LYS cc_start: 0.8800 (mmmm) cc_final: 0.8591 (mmtt) REVERT: E 129 ARG cc_start: 0.8846 (mmm160) cc_final: 0.8277 (mmm160) REVERT: F 25 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8507 (t0) REVERT: F 44 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9205 (mmmt) REVERT: F 74 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8907 (mt-10) REVERT: F 79 LYS cc_start: 0.9243 (mmmt) cc_final: 0.8819 (mtpp) REVERT: F 80 THR cc_start: 0.9361 (m) cc_final: 0.8855 (p) REVERT: F 88 TYR cc_start: 0.9061 (m-80) cc_final: 0.8804 (m-10) REVERT: F 92 ARG cc_start: 0.8963 (tmt-80) cc_final: 0.8757 (tmt-80) REVERT: G 120 MET cc_start: 0.8568 (mmm) cc_final: 0.8356 (mmm) REVERT: G 131 ARG cc_start: 0.8898 (mtp85) cc_final: 0.8559 (mtp85) REVERT: H 36 ARG cc_start: 0.9054 (mmp80) cc_final: 0.8822 (mmp80) REVERT: H 43 VAL cc_start: 0.7943 (t) cc_final: 0.7562 (t) REVERT: H 47 SER cc_start: 0.7850 (t) cc_final: 0.7615 (t) REVERT: H 49 LEU cc_start: 0.8036 (mp) cc_final: 0.7753 (mm) REVERT: H 53 GLU cc_start: 0.9319 (mt-10) cc_final: 0.9046 (mt-10) outliers start: 26 outliers final: 18 residues processed: 264 average time/residue: 0.1108 time to fit residues: 37.8841 Evaluate side-chains 270 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 59 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 55 optimal weight: 40.0000 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 61 optimal weight: 20.0000 chunk 6 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.058713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.042285 restraints weight = 55632.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.043563 restraints weight = 26949.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.044375 restraints weight = 17925.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.044880 restraints weight = 14189.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.045077 restraints weight = 12394.742| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9362 Z= 0.174 Angle : 0.719 9.851 13488 Z= 0.410 Chirality : 0.044 0.306 1549 Planarity : 0.005 0.046 1004 Dihedral : 31.009 146.813 2840 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.06 % Allowed : 31.38 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.33), residues: 563 helix: 1.43 (0.23), residues: 462 sheet: None (None), residues: 0 loop : -1.11 (0.49), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 40 TYR 0.016 0.002 TYR E 99 PHE 0.020 0.002 PHE A 78 HIS 0.005 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 ( 9362) covalent geometry : angle 0.71911 / 0.41 (13488) hydrogen bonds : bond 0.06028 / 3.97 ( 580) hydrogen bonds : angle 3.49394 / 2.56 ( 1477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 260 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8357 (mt) cc_final: 0.7512 (mt) REVERT: A 90 MET cc_start: 0.8729 (tmm) cc_final: 0.8284 (tmm) REVERT: A 112 ILE cc_start: 0.9694 (tp) cc_final: 0.9399 (pt) REVERT: A 120 MET cc_start: 0.8537 (mtm) cc_final: 0.8087 (mtm) REVERT: A 134 ARG cc_start: 0.8808 (tpp-160) cc_final: 0.8434 (tpp-160) REVERT: B 63 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8936 (mm-30) REVERT: B 68 ASP cc_start: 0.8519 (t70) cc_final: 0.8124 (t0) REVERT: B 77 LYS cc_start: 0.8292 (mttp) cc_final: 0.8027 (mmtm) REVERT: C 68 GLN cc_start: 0.9516 (mt0) cc_final: 0.9309 (tt0) REVERT: C 73 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8522 (tm-30) REVERT: C 77 ASP cc_start: 0.8978 (t70) cc_final: 0.8702 (t0) REVERT: C 85 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.8804 (mt0) REVERT: C 105 GLU cc_start: 0.8985 (tp30) cc_final: 0.8708 (mm-30) REVERT: C 129 ARG cc_start: 0.9259 (tpp80) cc_final: 0.8981 (tpp80) REVERT: D 44 LYS cc_start: 0.9292 (ttmm) cc_final: 0.9065 (mtpp) REVERT: D 53 GLU cc_start: 0.9119 (tp30) cc_final: 0.8772 (tp30) REVERT: E 62 ILE cc_start: 0.8858 (mt) cc_final: 0.8443 (tp) REVERT: E 120 MET cc_start: 0.8378 (mmm) cc_final: 0.7967 (mmm) REVERT: E 129 ARG cc_start: 0.8869 (mmm160) cc_final: 0.8247 (mmm160) REVERT: F 23 ARG cc_start: 0.8007 (ptm160) cc_final: 0.7447 (ptm-80) REVERT: F 31 LYS cc_start: 0.9330 (ttpp) cc_final: 0.8972 (ttmm) REVERT: F 44 LYS cc_start: 0.9488 (OUTLIER) cc_final: 0.9210 (mmmm) REVERT: F 52 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8177 (tm-30) REVERT: F 79 LYS cc_start: 0.9263 (mmmt) cc_final: 0.8868 (mtpp) REVERT: F 80 THR cc_start: 0.9420 (m) cc_final: 0.8839 (p) REVERT: F 88 TYR cc_start: 0.9050 (m-80) cc_final: 0.8777 (m-10) REVERT: G 90 MET cc_start: 0.8904 (tpp) cc_final: 0.8636 (tpp) REVERT: G 131 ARG cc_start: 0.8940 (mtp85) cc_final: 0.8580 (mtp85) REVERT: H 43 VAL cc_start: 0.7823 (t) cc_final: 0.7384 (t) REVERT: H 47 SER cc_start: 0.7933 (t) cc_final: 0.6085 (t) REVERT: H 53 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9050 (mt-10) REVERT: H 63 GLU cc_start: 0.9561 (tm-30) cc_final: 0.9352 (tm-30) REVERT: H 64 ASN cc_start: 0.9492 (p0) cc_final: 0.9281 (p0) outliers start: 25 outliers final: 17 residues processed: 264 average time/residue: 0.1114 time to fit residues: 37.6186 Evaluate side-chains 266 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 59 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 40.0000 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 30.0000 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.057815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.041105 restraints weight = 54082.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.042400 restraints weight = 26350.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.043221 restraints weight = 17503.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.043730 restraints weight = 13801.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.044017 restraints weight = 12047.087| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9362 Z= 0.202 Angle : 0.749 9.533 13488 Z= 0.426 Chirality : 0.044 0.307 1549 Planarity : 0.005 0.046 1004 Dihedral : 31.046 147.364 2840 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.87 % Allowed : 30.77 % Favored : 63.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.33), residues: 563 helix: 1.40 (0.23), residues: 461 sheet: None (None), residues: 0 loop : -1.17 (0.48), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 36 TYR 0.020 0.002 TYR E 99 PHE 0.016 0.002 PHE G 78 HIS 0.004 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 ( 9362) covalent geometry : angle 0.74925 / 0.43 (13488) hydrogen bonds : bond 0.06266 / 4.13 ( 580) hydrogen bonds : angle 3.58939 / 2.65 ( 1477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8759 (tmm) cc_final: 0.8240 (tmm) REVERT: A 112 ILE cc_start: 0.9715 (tp) cc_final: 0.9381 (pt) REVERT: A 120 MET cc_start: 0.8660 (mtm) cc_final: 0.8210 (mtm) REVERT: A 134 ARG cc_start: 0.8788 (tpp-160) cc_final: 0.8563 (mmp80) REVERT: B 44 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8660 (mmmm) REVERT: B 63 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9064 (mm-30) REVERT: B 68 ASP cc_start: 0.8313 (t70) cc_final: 0.8098 (t0) REVERT: B 77 LYS cc_start: 0.8314 (mttp) cc_final: 0.8046 (mmtm) REVERT: B 92 ARG cc_start: 0.8685 (ptm-80) cc_final: 0.8269 (ttp80) REVERT: C 73 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8549 (tm-30) REVERT: C 77 ASP cc_start: 0.9025 (t70) cc_final: 0.8751 (t0) REVERT: C 125 GLN cc_start: 0.9207 (mt0) cc_final: 0.8915 (mp10) REVERT: C 129 ARG cc_start: 0.9262 (tpp80) cc_final: 0.8998 (tpp80) REVERT: D 44 LYS cc_start: 0.9300 (ttmm) cc_final: 0.9029 (mmmm) REVERT: D 53 GLU cc_start: 0.9203 (tp30) cc_final: 0.8847 (tp30) REVERT: E 115 LYS cc_start: 0.9595 (mmmm) cc_final: 0.9324 (mmmm) REVERT: E 129 ARG cc_start: 0.8938 (mmm160) cc_final: 0.8375 (mmm160) REVERT: F 31 LYS cc_start: 0.9339 (ttpp) cc_final: 0.9108 (ttmm) REVERT: F 44 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9214 (mmmm) REVERT: F 52 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8169 (tm-30) REVERT: F 79 LYS cc_start: 0.9265 (mmmt) cc_final: 0.8869 (mtpp) REVERT: F 80 THR cc_start: 0.9420 (m) cc_final: 0.8850 (p) REVERT: F 88 TYR cc_start: 0.9062 (m-80) cc_final: 0.8750 (m-10) REVERT: G 70 LEU cc_start: 0.9256 (mt) cc_final: 0.8988 (mt) REVERT: G 131 ARG cc_start: 0.8938 (mtp85) cc_final: 0.8565 (mtp85) REVERT: H 49 LEU cc_start: 0.8066 (mm) cc_final: 0.7762 (mm) REVERT: H 53 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9040 (mt-10) outliers start: 29 outliers final: 22 residues processed: 255 average time/residue: 0.1166 time to fit residues: 37.8807 Evaluate side-chains 255 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 232 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain H residue 59 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.057839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.041245 restraints weight = 56720.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.042556 restraints weight = 27986.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.043418 restraints weight = 18600.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.043862 restraints weight = 14598.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.044203 restraints weight = 12830.431| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9362 Z= 0.180 Angle : 0.762 14.905 13488 Z= 0.425 Chirality : 0.045 0.320 1549 Planarity : 0.005 0.061 1004 Dihedral : 31.083 148.272 2840 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.26 % Allowed : 32.59 % Favored : 62.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.34), residues: 563 helix: 1.39 (0.23), residues: 461 sheet: None (None), residues: 0 loop : -1.33 (0.48), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 36 TYR 0.015 0.002 TYR H 72 PHE 0.023 0.002 PHE G 78 HIS 0.005 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 ( 9362) covalent geometry : angle 0.76243 / 0.43 (13488) hydrogen bonds : bond 0.06026 / 3.96 ( 580) hydrogen bonds : angle 3.55192 / 2.61 ( 1477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9604 (tp-100) cc_final: 0.9396 (mm110) REVERT: A 90 MET cc_start: 0.8739 (tmm) cc_final: 0.8220 (tmm) REVERT: A 112 ILE cc_start: 0.9716 (tp) cc_final: 0.9415 (pt) REVERT: A 120 MET cc_start: 0.8649 (mtm) cc_final: 0.8129 (mtm) REVERT: A 125 GLN cc_start: 0.9325 (mt0) cc_final: 0.8953 (mm-40) REVERT: B 30 THR cc_start: 0.9030 (p) cc_final: 0.8789 (t) REVERT: B 44 LYS cc_start: 0.8853 (mmmt) cc_final: 0.8580 (mmmm) REVERT: B 63 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8979 (mm-30) REVERT: B 68 ASP cc_start: 0.8369 (t70) cc_final: 0.8089 (t0) REVERT: B 91 LYS cc_start: 0.9434 (mmmm) cc_final: 0.9201 (mmmm) REVERT: B 92 ARG cc_start: 0.8679 (ptm-80) cc_final: 0.8298 (ttp80) REVERT: C 73 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8529 (tm-30) REVERT: C 77 ASP cc_start: 0.9043 (t70) cc_final: 0.8765 (t0) REVERT: C 105 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8812 (mm-30) REVERT: C 125 GLN cc_start: 0.9257 (mt0) cc_final: 0.8931 (mp10) REVERT: C 129 ARG cc_start: 0.9280 (tpp80) cc_final: 0.8844 (ttp80) REVERT: D 53 GLU cc_start: 0.9196 (tp30) cc_final: 0.8847 (tp30) REVERT: D 72 TYR cc_start: 0.9225 (m-80) cc_final: 0.8721 (m-80) REVERT: D 79 LYS cc_start: 0.8798 (mmmt) cc_final: 0.8470 (mmmm) REVERT: E 73 GLU cc_start: 0.8860 (tt0) cc_final: 0.8627 (tm-30) REVERT: E 76 GLN cc_start: 0.9297 (pt0) cc_final: 0.8876 (pp30) REVERT: E 115 LYS cc_start: 0.9613 (mmmm) cc_final: 0.9336 (mmmm) REVERT: E 120 MET cc_start: 0.8705 (mmm) cc_final: 0.8077 (mmm) REVERT: E 129 ARG cc_start: 0.8910 (mmm160) cc_final: 0.8385 (mmm160) REVERT: F 31 LYS cc_start: 0.9313 (ttpp) cc_final: 0.9086 (ttmm) REVERT: F 44 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.9208 (mmmm) REVERT: F 52 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8187 (tm-30) REVERT: F 79 LYS cc_start: 0.9247 (mmmt) cc_final: 0.8828 (mtpp) REVERT: F 80 THR cc_start: 0.9392 (m) cc_final: 0.8817 (p) REVERT: F 88 TYR cc_start: 0.9016 (m-80) cc_final: 0.8712 (m-10) REVERT: G 78 PHE cc_start: 0.8560 (t80) cc_final: 0.6969 (t80) REVERT: G 108 ASN cc_start: 0.9655 (t0) cc_final: 0.9447 (t0) REVERT: G 131 ARG cc_start: 0.8884 (mtp85) cc_final: 0.8493 (mtp85) REVERT: H 49 LEU cc_start: 0.8035 (mm) cc_final: 0.7746 (mm) REVERT: H 53 GLU cc_start: 0.9305 (mt-10) cc_final: 0.9004 (mt-10) outliers start: 26 outliers final: 23 residues processed: 248 average time/residue: 0.1149 time to fit residues: 36.5579 Evaluate side-chains 256 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 59 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 30 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.056740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.040094 restraints weight = 55479.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.041319 restraints weight = 27881.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.042099 restraints weight = 18741.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.042523 restraints weight = 14868.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 68)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.042850 restraints weight = 13117.268| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9362 Z= 0.235 Angle : 0.806 15.907 13488 Z= 0.447 Chirality : 0.045 0.318 1549 Planarity : 0.008 0.170 1004 Dihedral : 31.166 148.933 2840 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.87 % Allowed : 33.60 % Favored : 60.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.33), residues: 563 helix: 1.32 (0.23), residues: 462 sheet: None (None), residues: 0 loop : -1.28 (0.48), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 40 TYR 0.025 0.002 TYR E 99 PHE 0.046 0.003 PHE G 78 HIS 0.004 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 ( 9362) covalent geometry : angle 0.80562 / 0.45 (13488) hydrogen bonds : bond 0.06663 / 4.42 ( 580) hydrogen bonds : angle 3.69593 / 2.69 ( 1477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9606 (tp40) cc_final: 0.9322 (mm110) REVERT: A 90 MET cc_start: 0.8743 (tmm) cc_final: 0.8230 (tmm) REVERT: A 112 ILE cc_start: 0.9724 (tp) cc_final: 0.9400 (pt) REVERT: A 120 MET cc_start: 0.8706 (mtm) cc_final: 0.8229 (mtm) REVERT: A 125 GLN cc_start: 0.9309 (mt0) cc_final: 0.8944 (mm-40) REVERT: B 44 LYS cc_start: 0.9013 (mmmt) cc_final: 0.8653 (mmmm) REVERT: B 63 GLU cc_start: 0.9314 (mt-10) cc_final: 0.9062 (mm-30) REVERT: B 68 ASP cc_start: 0.8424 (t70) cc_final: 0.8157 (t0) REVERT: B 77 LYS cc_start: 0.9127 (tppt) cc_final: 0.8525 (mppt) REVERT: B 91 LYS cc_start: 0.9433 (mmmm) cc_final: 0.9169 (mmmm) REVERT: B 92 ARG cc_start: 0.8664 (ptm-80) cc_final: 0.8347 (ttp80) REVERT: C 63 ARG cc_start: 0.8308 (mmp-170) cc_final: 0.8021 (mmp-170) REVERT: C 70 LEU cc_start: 0.9452 (tt) cc_final: 0.9156 (tt) REVERT: C 73 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8583 (tm-30) REVERT: C 77 ASP cc_start: 0.9061 (t70) cc_final: 0.8784 (t0) REVERT: C 85 GLN cc_start: 0.9402 (mt0) cc_final: 0.8582 (mt0) REVERT: C 105 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8830 (mm-30) REVERT: C 125 GLN cc_start: 0.9221 (mt0) cc_final: 0.8930 (mp10) REVERT: D 79 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8510 (mmmm) REVERT: E 76 GLN cc_start: 0.9337 (pt0) cc_final: 0.8878 (pp30) REVERT: E 115 LYS cc_start: 0.9615 (mmmm) cc_final: 0.9360 (mmmm) REVERT: E 120 MET cc_start: 0.8693 (mmm) cc_final: 0.8431 (mmm) REVERT: E 129 ARG cc_start: 0.8938 (mmm160) cc_final: 0.8391 (mmm160) REVERT: F 31 LYS cc_start: 0.9339 (ttpp) cc_final: 0.9114 (ttmm) REVERT: F 44 LYS cc_start: 0.9492 (OUTLIER) cc_final: 0.9113 (mmmm) REVERT: F 52 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8177 (tm-30) REVERT: F 79 LYS cc_start: 0.9271 (mmmt) cc_final: 0.8877 (mtpp) REVERT: F 80 THR cc_start: 0.9483 (m) cc_final: 0.8962 (p) REVERT: F 88 TYR cc_start: 0.9092 (m-80) cc_final: 0.8784 (m-10) REVERT: F 92 ARG cc_start: 0.9059 (tmt-80) cc_final: 0.8756 (ttt90) REVERT: G 131 ARG cc_start: 0.8993 (mtp85) cc_final: 0.8681 (mtp85) REVERT: H 49 LEU cc_start: 0.7986 (mm) cc_final: 0.7679 (mm) REVERT: H 53 GLU cc_start: 0.9368 (mt-10) cc_final: 0.9078 (mt-10) outliers start: 29 outliers final: 26 residues processed: 243 average time/residue: 0.1131 time to fit residues: 34.9250 Evaluate side-chains 254 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 227 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 78 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 15 optimal weight: 0.3980 chunk 66 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.057996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.041344 restraints weight = 54226.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.042600 restraints weight = 27252.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.043400 restraints weight = 18299.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.043900 restraints weight = 14484.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.044103 restraints weight = 12657.688| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9362 Z= 0.176 Angle : 0.795 16.788 13488 Z= 0.437 Chirality : 0.045 0.335 1549 Planarity : 0.006 0.087 1004 Dihedral : 31.177 150.306 2840 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 6.07 % Allowed : 34.41 % Favored : 59.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.33), residues: 563 helix: 1.31 (0.23), residues: 460 sheet: None (None), residues: 0 loop : -1.05 (0.50), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 40 TYR 0.018 0.002 TYR A 99 PHE 0.013 0.002 PHE C 78 HIS 0.004 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 ( 9362) covalent geometry : angle 0.79506 / 0.44 (13488) hydrogen bonds : bond 0.05913 / 3.90 ( 580) hydrogen bonds : angle 3.62865 / 2.67 ( 1477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8707 (mm) cc_final: 0.8414 (mm) REVERT: A 68 GLN cc_start: 0.9567 (OUTLIER) cc_final: 0.9211 (mm-40) REVERT: A 74 ILE cc_start: 0.9754 (tt) cc_final: 0.9531 (tt) REVERT: A 90 MET cc_start: 0.8706 (tmm) cc_final: 0.8158 (tmm) REVERT: A 112 ILE cc_start: 0.9699 (tp) cc_final: 0.9397 (pt) REVERT: A 120 MET cc_start: 0.8637 (mtm) cc_final: 0.8157 (mtm) REVERT: A 125 GLN cc_start: 0.9313 (mt0) cc_final: 0.8954 (mm-40) REVERT: B 30 THR cc_start: 0.9005 (p) cc_final: 0.8761 (t) REVERT: B 44 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8668 (mmmm) REVERT: B 63 GLU cc_start: 0.9300 (mt-10) cc_final: 0.9012 (mm-30) REVERT: B 68 ASP cc_start: 0.8396 (t70) cc_final: 0.8135 (t0) REVERT: B 91 LYS cc_start: 0.9429 (mmmm) cc_final: 0.9157 (mmmm) REVERT: B 92 ARG cc_start: 0.8640 (ptm-80) cc_final: 0.8312 (ttp80) REVERT: C 63 ARG cc_start: 0.8239 (mmp-170) cc_final: 0.7967 (mmp-170) REVERT: C 73 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8557 (tm-30) REVERT: C 77 ASP cc_start: 0.9056 (t70) cc_final: 0.8782 (t0) REVERT: C 85 GLN cc_start: 0.9386 (mt0) cc_final: 0.8520 (mt0) REVERT: C 93 GLN cc_start: 0.9035 (tt0) cc_final: 0.8814 (tt0) REVERT: C 105 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8809 (mm-30) REVERT: C 125 GLN cc_start: 0.9232 (mt0) cc_final: 0.8909 (mp10) REVERT: C 129 ARG cc_start: 0.9245 (tpp80) cc_final: 0.8840 (ttp80) REVERT: D 53 GLU cc_start: 0.9208 (tp30) cc_final: 0.8972 (tp30) REVERT: D 79 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8491 (mmmm) REVERT: E 73 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8764 (tt0) REVERT: E 76 GLN cc_start: 0.9292 (pt0) cc_final: 0.8867 (pp30) REVERT: E 79 LYS cc_start: 0.8384 (tptp) cc_final: 0.8072 (tptt) REVERT: E 115 LYS cc_start: 0.9618 (mmmm) cc_final: 0.9365 (mmmm) REVERT: E 120 MET cc_start: 0.8709 (mmm) cc_final: 0.8175 (mmm) REVERT: E 129 ARG cc_start: 0.8906 (mmm160) cc_final: 0.8358 (mmm160) REVERT: F 31 LYS cc_start: 0.9326 (ttpp) cc_final: 0.9094 (ttmm) REVERT: F 44 LYS cc_start: 0.9468 (OUTLIER) cc_final: 0.9197 (mmmm) REVERT: F 52 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8163 (tm-30) REVERT: F 79 LYS cc_start: 0.9283 (mmmt) cc_final: 0.8847 (mtpp) REVERT: F 80 THR cc_start: 0.9436 (m) cc_final: 0.8843 (p) REVERT: F 88 TYR cc_start: 0.9022 (m-80) cc_final: 0.8754 (m-10) REVERT: G 131 ARG cc_start: 0.8999 (mtp85) cc_final: 0.8607 (mtp85) REVERT: H 49 LEU cc_start: 0.7988 (mm) cc_final: 0.7668 (mm) REVERT: H 53 GLU cc_start: 0.9342 (mt-10) cc_final: 0.9031 (mt-10) outliers start: 30 outliers final: 22 residues processed: 253 average time/residue: 0.1128 time to fit residues: 36.5282 Evaluate side-chains 260 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 78 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 74 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.058244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.041631 restraints weight = 55022.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.042887 restraints weight = 27531.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.043679 restraints weight = 18486.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.044120 restraints weight = 14669.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.044467 restraints weight = 12937.988| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9362 Z= 0.177 Angle : 0.823 17.568 13488 Z= 0.447 Chirality : 0.045 0.341 1549 Planarity : 0.005 0.066 1004 Dihedral : 31.150 150.716 2840 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.26 % Allowed : 36.23 % Favored : 58.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.33), residues: 563 helix: 1.36 (0.23), residues: 460 sheet: None (None), residues: 0 loop : -1.10 (0.50), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 40 TYR 0.021 0.002 TYR H 72 PHE 0.017 0.002 PHE A 84 HIS 0.004 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 ( 9362) covalent geometry : angle 0.82306 / 0.45 (13488) hydrogen bonds : bond 0.05818 / 3.86 ( 580) hydrogen bonds : angle 3.60170 / 2.65 ( 1477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 239 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9553 (OUTLIER) cc_final: 0.9206 (mm-40) REVERT: A 74 ILE cc_start: 0.9764 (tt) cc_final: 0.9531 (tt) REVERT: A 90 MET cc_start: 0.8666 (tmm) cc_final: 0.8172 (tmm) REVERT: A 112 ILE cc_start: 0.9696 (tp) cc_final: 0.9401 (pt) REVERT: A 120 MET cc_start: 0.8586 (mtm) cc_final: 0.8119 (mtm) REVERT: A 125 GLN cc_start: 0.9294 (mt0) cc_final: 0.8950 (mm-40) REVERT: B 30 THR cc_start: 0.8990 (p) cc_final: 0.8774 (t) REVERT: B 44 LYS cc_start: 0.9086 (mmmt) cc_final: 0.8781 (mmmm) REVERT: B 63 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8998 (mm-30) REVERT: B 68 ASP cc_start: 0.8382 (t70) cc_final: 0.8149 (t0) REVERT: B 91 LYS cc_start: 0.9422 (mmmm) cc_final: 0.9131 (mmmm) REVERT: B 92 ARG cc_start: 0.8627 (ptm-80) cc_final: 0.8300 (ttp80) REVERT: C 63 ARG cc_start: 0.8190 (mmp-170) cc_final: 0.7908 (mmp-170) REVERT: C 73 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8570 (tm-30) REVERT: C 77 ASP cc_start: 0.9027 (t70) cc_final: 0.8748 (t0) REVERT: C 85 GLN cc_start: 0.9360 (mt0) cc_final: 0.8560 (mt0) REVERT: C 93 GLN cc_start: 0.9032 (tt0) cc_final: 0.8796 (tt0) REVERT: C 105 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8779 (mm-30) REVERT: C 125 GLN cc_start: 0.9189 (mt0) cc_final: 0.8893 (mp10) REVERT: C 128 ARG cc_start: 0.9235 (mtp85) cc_final: 0.8991 (mtp85) REVERT: C 129 ARG cc_start: 0.9213 (tpp80) cc_final: 0.8829 (tpp80) REVERT: D 53 GLU cc_start: 0.9166 (tp30) cc_final: 0.8935 (tp30) REVERT: D 72 TYR cc_start: 0.9198 (m-80) cc_final: 0.8658 (m-80) REVERT: D 79 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8541 (mmmm) REVERT: E 76 GLN cc_start: 0.9275 (pt0) cc_final: 0.8783 (pp30) REVERT: E 79 LYS cc_start: 0.8449 (tptp) cc_final: 0.8127 (tptt) REVERT: E 115 LYS cc_start: 0.9625 (mmmm) cc_final: 0.9372 (mmmm) REVERT: E 129 ARG cc_start: 0.8922 (mmm160) cc_final: 0.8347 (mmm160) REVERT: F 23 ARG cc_start: 0.7601 (ptm160) cc_final: 0.7285 (ptm-80) REVERT: F 31 LYS cc_start: 0.9338 (ttpp) cc_final: 0.9085 (ttmm) REVERT: F 35 ARG cc_start: 0.9365 (ttp80) cc_final: 0.8861 (ttm-80) REVERT: F 44 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9192 (mmmm) REVERT: F 52 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8145 (tm-30) REVERT: F 79 LYS cc_start: 0.9299 (mmmt) cc_final: 0.8858 (mtpp) REVERT: F 80 THR cc_start: 0.9449 (m) cc_final: 0.8838 (p) REVERT: F 88 TYR cc_start: 0.9024 (m-80) cc_final: 0.8756 (m-10) REVERT: F 92 ARG cc_start: 0.9020 (tmt-80) cc_final: 0.8705 (ttt90) REVERT: G 131 ARG cc_start: 0.9033 (mtp85) cc_final: 0.8636 (mtp85) REVERT: H 49 LEU cc_start: 0.7924 (mm) cc_final: 0.7449 (mm) REVERT: H 53 GLU cc_start: 0.9326 (mt-10) cc_final: 0.9003 (mt-10) outliers start: 26 outliers final: 20 residues processed: 244 average time/residue: 0.1314 time to fit residues: 40.4150 Evaluate side-chains 255 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 124 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 71 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.058132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.041320 restraints weight = 53844.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.042634 restraints weight = 27024.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.043453 restraints weight = 18126.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.043971 restraints weight = 14292.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.044246 restraints weight = 12443.803| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9362 Z= 0.178 Angle : 0.832 19.220 13488 Z= 0.448 Chirality : 0.045 0.333 1549 Planarity : 0.006 0.087 1004 Dihedral : 31.124 151.163 2840 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.25 % Allowed : 37.65 % Favored : 58.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.33), residues: 563 helix: 1.28 (0.23), residues: 460 sheet: None (None), residues: 0 loop : -1.22 (0.51), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 36 TYR 0.024 0.002 TYR A 99 PHE 0.015 0.002 PHE G 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 ( 9362) covalent geometry : angle 0.83232 / 0.45 (13488) hydrogen bonds : bond 0.05756 / 3.82 ( 580) hydrogen bonds : angle 3.61402 / 2.67 ( 1477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9544 (tp40) cc_final: 0.9212 (mm-40) REVERT: A 74 ILE cc_start: 0.9756 (tt) cc_final: 0.9515 (tt) REVERT: A 90 MET cc_start: 0.8657 (tmm) cc_final: 0.8040 (tmm) REVERT: A 112 ILE cc_start: 0.9694 (tp) cc_final: 0.9395 (pt) REVERT: A 120 MET cc_start: 0.8598 (mtm) cc_final: 0.8110 (mtm) REVERT: A 125 GLN cc_start: 0.9310 (mt0) cc_final: 0.8960 (mm-40) REVERT: B 44 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8878 (mmmt) REVERT: B 63 GLU cc_start: 0.9300 (mt-10) cc_final: 0.9010 (mm-30) REVERT: B 68 ASP cc_start: 0.8478 (t70) cc_final: 0.8187 (t0) REVERT: B 91 LYS cc_start: 0.9411 (mmmm) cc_final: 0.9114 (mmmm) REVERT: B 92 ARG cc_start: 0.8645 (ptm-80) cc_final: 0.8334 (ttp80) REVERT: C 63 ARG cc_start: 0.8180 (mmp-170) cc_final: 0.7887 (mmp-170) REVERT: C 73 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8607 (tm-30) REVERT: C 77 ASP cc_start: 0.9047 (t70) cc_final: 0.8796 (t0) REVERT: C 85 GLN cc_start: 0.9369 (mt0) cc_final: 0.8529 (mt0) REVERT: C 93 GLN cc_start: 0.9050 (tt0) cc_final: 0.8825 (tt0) REVERT: C 105 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8681 (mm-30) REVERT: C 120 MET cc_start: 0.8895 (mmm) cc_final: 0.8468 (mmm) REVERT: C 125 GLN cc_start: 0.9216 (mt0) cc_final: 0.8894 (mp10) REVERT: C 128 ARG cc_start: 0.9161 (mtp85) cc_final: 0.8894 (mtp85) REVERT: C 129 ARG cc_start: 0.9221 (tpp80) cc_final: 0.8890 (tpp80) REVERT: D 53 GLU cc_start: 0.9188 (tp30) cc_final: 0.8954 (tp30) REVERT: D 79 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8549 (mmmm) REVERT: E 76 GLN cc_start: 0.9268 (pt0) cc_final: 0.8771 (pp30) REVERT: E 79 LYS cc_start: 0.8444 (tptp) cc_final: 0.8138 (tptt) REVERT: E 115 LYS cc_start: 0.9623 (mmmm) cc_final: 0.9368 (mmmm) REVERT: E 120 MET cc_start: 0.8731 (mmm) cc_final: 0.8137 (mmm) REVERT: E 129 ARG cc_start: 0.8938 (mmm160) cc_final: 0.8346 (mmm160) REVERT: F 31 LYS cc_start: 0.9336 (ttpp) cc_final: 0.9080 (ttmm) REVERT: F 35 ARG cc_start: 0.9368 (ttp80) cc_final: 0.8874 (ttm-80) REVERT: F 44 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9190 (mmmm) REVERT: F 52 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8128 (tm-30) REVERT: F 79 LYS cc_start: 0.9296 (mmmt) cc_final: 0.8845 (mtpp) REVERT: F 80 THR cc_start: 0.9432 (m) cc_final: 0.8814 (p) REVERT: F 88 TYR cc_start: 0.9004 (m-80) cc_final: 0.8738 (m-10) REVERT: F 92 ARG cc_start: 0.9043 (tmt-80) cc_final: 0.8739 (ttt90) REVERT: G 131 ARG cc_start: 0.9028 (mtp85) cc_final: 0.8634 (mtp85) REVERT: H 53 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8973 (mt-10) outliers start: 21 outliers final: 17 residues processed: 242 average time/residue: 0.1304 time to fit residues: 39.9559 Evaluate side-chains 249 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 78 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 65 optimal weight: 40.0000 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.056925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.040348 restraints weight = 53549.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.041625 restraints weight = 26578.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.042451 restraints weight = 17661.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.042951 restraints weight = 13910.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.043252 restraints weight = 12133.447| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9362 Z= 0.200 Angle : 0.848 19.663 13488 Z= 0.457 Chirality : 0.045 0.332 1549 Planarity : 0.006 0.101 1004 Dihedral : 31.153 151.474 2840 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.64 % Allowed : 38.66 % Favored : 57.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.34), residues: 563 helix: 1.32 (0.23), residues: 460 sheet: None (None), residues: 0 loop : -1.25 (0.49), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG H 36 TYR 0.015 0.002 TYR D 72 PHE 0.016 0.002 PHE G 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 ( 9362) covalent geometry : angle 0.84777 / 0.46 (13488) hydrogen bonds : bond 0.05990 / 3.98 ( 580) hydrogen bonds : angle 3.70542 / 2.72 ( 1477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1896.90 seconds wall clock time: 33 minutes 11.84 seconds (1991.84 seconds total)