Starting phenix.real_space_refine on Fri Sep 11 20:14:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r5r_14334/09_2026/7r5r_14334.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r5r_14334/09_2026/7r5r_14334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r5r_14334/09_2026/7r5r_14334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r5r_14334/09_2026/7r5r_14334.map" model { file = "/net/cci-nas-00/data/ceres_data/7r5r_14334/09_2026/7r5r_14334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r5r_14334/09_2026/7r5r_14334.cif" } resolution = 2.44 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= -0.001 sd= 0.049 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 266 5.49 5 S 8 5.16 5 C 6528 2.51 5 N 2145 2.21 5 O 2678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 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: 11625 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 799 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 96} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 770 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 784 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 97} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2729 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain: "J" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2724 Classifications: {'DNA': 133} Link IDs: {'rna3p': 132} Chain breaks: 1 Chain: "K" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 178 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "L" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 185 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Time building chain proxies: 2.49, per 1000 atoms: 0.21 Number of scatterers: 11625 At special positions: 0 Unit cell: (81.888, 116.861, 119.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 P 266 15.00 O 2678 8.00 N 2145 7.00 C 6528 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: 0.85 Conformation dependent library (CDL) restraints added in 222.7 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 11 sheets defined 68.5% alpha, 2.8% beta 124 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 removed outlier: 4.293A pdb=" N LYS A 49 " --> pdb=" O GLN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.751A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 122 through 134 removed outlier: 3.703A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.666A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.063A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.515A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.640A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.687A pdb=" N MET D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 47 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.851A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR E 79 " --> pdb=" O CYS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 117 Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.656A pdb=" N VAL E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.646A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.944A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.853A pdb=" N ASN A 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.437A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.319A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 86 removed outlier: 6.925A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.306A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'L' and resid 516 through 517 389 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 286 hydrogen bonds 572 hydrogen bond angles 0 basepair planarities 124 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2058 1.33 - 1.45: 4086 1.45 - 1.57: 5694 1.57 - 1.69: 527 1.69 - 1.81: 14 Bond restraints: 12379 Sorted by residual: bond pdb=" O3' DA I 20 " pdb=" P DC I 21 " ideal model delta sigma weight residual 1.607 1.683 -0.076 1.20e-02 6.94e+03 3.98e+01 bond pdb=" C1' DG J 34 " pdb=" N9 DG J 34 " ideal model delta sigma weight residual 1.468 1.388 0.080 1.40e-02 5.10e+03 3.24e+01 bond pdb=" C1' DC J 20 " pdb=" N1 DC J 20 " ideal model delta sigma weight residual 1.468 1.543 -0.075 1.40e-02 5.10e+03 2.87e+01 bond pdb=" C1' DG I -20 " pdb=" N9 DG I -20 " ideal model delta sigma weight residual 1.468 1.394 0.074 1.40e-02 5.10e+03 2.78e+01 bond pdb=" C1' DC I -34 " pdb=" N1 DC I -34 " ideal model delta sigma weight residual 1.468 1.542 -0.074 1.40e-02 5.10e+03 2.78e+01 ... (remaining 12374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 17780 3.13 - 6.25: 71 6.25 - 9.38: 5 9.38 - 12.50: 2 12.50 - 15.63: 2 Bond angle restraints: 17860 Sorted by residual: angle pdb=" C3' DA I 17 " pdb=" O3' DA I 17 " pdb=" P DT I 18 " ideal model delta sigma weight residual 119.70 134.92 -15.22 1.20e+00 6.94e-01 1.61e+02 angle pdb=" C4' DA J -18 " pdb=" C3' DA J -18 " pdb=" O3' DA J -18 " ideal model delta sigma weight residual 109.70 94.07 15.63 2.50e+00 1.60e-01 3.91e+01 angle pdb=" C3' DA J -18 " pdb=" O3' DA J -18 " pdb=" P DT J -17 " ideal model delta sigma weight residual 119.70 126.43 -6.73 1.20e+00 6.94e-01 3.15e+01 angle pdb=" C3' DC I 19 " pdb=" C2' DC I 19 " pdb=" C1' DC I 19 " ideal model delta sigma weight residual 102.50 108.47 -5.97 1.20e+00 6.94e-01 2.47e+01 angle pdb=" C3' DG J -16 " pdb=" O3' DG J -16 " pdb=" P DT J -15 " ideal model delta sigma weight residual 119.70 125.57 -5.87 1.20e+00 6.94e-01 2.39e+01 ... (remaining 17855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 5618 35.80 - 71.60: 1193 71.60 - 107.40: 19 107.40 - 143.19: 0 143.19 - 178.99: 2 Dihedral angle restraints: 6832 sinusoidal: 4587 harmonic: 2245 Sorted by residual: dihedral pdb=" C4' DA J -49 " pdb=" C3' DA J -49 " pdb=" O3' DA J -49 " pdb=" P DG J -48 " ideal model delta sinusoidal sigma weight residual 220.00 41.01 178.99 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J -16 " pdb=" C3' DG J -16 " pdb=" O3' DG J -16 " pdb=" P DT J -15 " ideal model delta sinusoidal sigma weight residual -140.00 30.40 -170.40 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA GLY E 134 " pdb=" C GLY E 134 " pdb=" N LEU E 135 " pdb=" CA LEU E 135 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1897 0.084 - 0.168: 126 0.168 - 0.252: 7 0.252 - 0.337: 2 0.337 - 0.421: 1 Chirality restraints: 2033 Sorted by residual: chirality pdb=" C3' DA J -18 " pdb=" C4' DA J -18 " pdb=" O3' DA J -18 " pdb=" C2' DA J -18 " both_signs ideal model delta sigma weight residual False -2.73 -3.15 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C3' DT I 18 " pdb=" C4' DT I 18 " pdb=" O3' DT I 18 " pdb=" C2' DT I 18 " both_signs ideal model delta sigma weight residual False -2.73 -3.04 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C4' DT I 18 " pdb=" C5' DT I 18 " pdb=" O4' DT I 18 " pdb=" C3' DT I 18 " both_signs ideal model delta sigma weight residual False -2.53 -2.24 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 2030 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J -16 " -0.019 2.00e-02 2.50e+03 2.08e-02 1.29e+01 pdb=" N9 DG J -16 " 0.045 2.00e-02 2.50e+03 pdb=" C8 DG J -16 " -0.025 2.00e-02 2.50e+03 pdb=" N7 DG J -16 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG J -16 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG J -16 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG J -16 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DG J -16 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG J -16 " -0.041 2.00e-02 2.50e+03 pdb=" N2 DG J -16 " 0.015 2.00e-02 2.50e+03 pdb=" N3 DG J -16 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DG J -16 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -19 " 0.015 2.00e-02 2.50e+03 1.93e-02 1.11e+01 pdb=" N9 DG J -19 " 0.002 2.00e-02 2.50e+03 pdb=" C8 DG J -19 " -0.027 2.00e-02 2.50e+03 pdb=" N7 DG J -19 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG J -19 " 0.030 2.00e-02 2.50e+03 pdb=" C6 DG J -19 " 0.042 2.00e-02 2.50e+03 pdb=" O6 DG J -19 " -0.019 2.00e-02 2.50e+03 pdb=" N1 DG J -19 " -0.014 2.00e-02 2.50e+03 pdb=" C2 DG J -19 " -0.009 2.00e-02 2.50e+03 pdb=" N2 DG J -19 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG J -19 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DG J -19 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " 0.013 2.00e-02 2.50e+03 1.94e-02 1.03e+01 pdb=" N9 DA I 20 " -0.031 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.024 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " -0.044 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " 0.015 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.015 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1514 2.76 - 3.30: 9716 3.30 - 3.83: 21549 3.83 - 4.37: 25862 4.37 - 4.90: 37546 Nonbonded interactions: 96187 Sorted by model distance: nonbonded pdb=" OH TYR C 39 " pdb=" OE2 GLU D 71 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR A 113 " pdb=" OD2 ASP A 125 " model vdw 2.259 3.040 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.273 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.283 3.040 nonbonded pdb=" OG1 THR E 113 " pdb=" OD2 ASP E 125 " model vdw 2.334 3.040 ... (remaining 96182 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 46 through 139) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 111) selection = (chain 'G' and resid 15 through 111) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and resid 515 through 535) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.990 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.080 Find NCS groups from input model: 0.130 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:8.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3945 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 : 0.006 0.080 12379 Z= 0.511 Angle : 0.793 15.627 17860 Z= 0.708 Chirality : 0.046 0.421 2033 Planarity : 0.004 0.041 1328 Dihedral : 26.939 178.993 5382 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.31 % Allowed : 12.13 % Favored : 87.56 % 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: -0.10 (0.27), residues: 759 helix: 1.05 (0.20), residues: 533 sheet: None (None), residues: 0 loop : -2.86 (0.29), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 23 TYR 0.006 0.001 TYR B 51 PHE 0.007 0.001 PHE H 70 TRP 0.004 0.001 TRP E 86 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.51 (12379) covalent geometry : angle 0.79309 / 0.71 (17860) hydrogen bonds : bond 0.10583 / 7.09 ( 675) hydrogen bonds : angle 3.56051 / 2.59 ( 1724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.341 Fit side-chains REVERT: B 31 LYS cc_start: 0.5334 (ttmm) cc_final: 0.4862 (tttp) REVERT: B 84 MET cc_start: 0.5751 (mmm) cc_final: 0.5455 (mmm) REVERT: B 91 LYS cc_start: 0.7261 (ttmm) cc_final: 0.6527 (ttpt) REVERT: C 99 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6787 (mtp85) REVERT: D 68 ASP cc_start: 0.5710 (t0) cc_final: 0.5390 (t0) REVERT: G 41 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6423 (mp0) REVERT: G 77 ARG cc_start: 0.7094 (mtm-85) cc_final: 0.6794 (mtm-85) REVERT: H 86 ARG cc_start: 0.6084 (mmt90) cc_final: 0.5814 (mmt90) outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 1.0378 time to fit residues: 145.2514 Evaluate side-chains 113 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 45 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 45 GLN B 93 GLN C 94 ASN E 87 GLN F 93 GLN G 73 ASN G 94 ASN H 84 ASN H 95 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.155421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.106982 restraints weight = 16274.471| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.38 r_work: 0.3268 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12379 Z= 0.149 Angle : 0.618 8.170 17860 Z= 0.372 Chirality : 0.044 0.267 2033 Planarity : 0.004 0.036 1328 Dihedral : 30.154 178.352 3885 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.87 % Allowed : 16.95 % Favored : 81.18 % 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 (0.29), residues: 759 helix: 2.16 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -2.35 (0.31), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 23 TYR 0.007 0.001 TYR G 50 PHE 0.007 0.001 PHE F 61 TRP 0.004 0.001 TRP A 47 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.15 (12379) covalent geometry : angle 0.61763 / 0.37 (17860) hydrogen bonds : bond 0.05915 / 3.97 ( 675) hydrogen bonds : angle 2.78048 / 1.98 ( 1724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.265 Fit side-chains REVERT: B 31 LYS cc_start: 0.7738 (ttmm) cc_final: 0.7364 (tttp) REVERT: B 91 LYS cc_start: 0.8989 (ttmm) cc_final: 0.8284 (ttpt) REVERT: D 68 ASP cc_start: 0.8786 (t0) cc_final: 0.8429 (t0) outliers start: 12 outliers final: 6 residues processed: 122 average time/residue: 0.9780 time to fit residues: 124.9639 Evaluate side-chains 113 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain H residue 46 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 0.0050 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN F 75 HIS G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.149256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.099003 restraints weight = 16080.484| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.38 r_work: 0.3136 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12379 Z= 0.222 Angle : 0.723 8.822 17860 Z= 0.411 Chirality : 0.050 0.299 2033 Planarity : 0.005 0.043 1328 Dihedral : 30.640 179.893 3885 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.95 % Allowed : 15.86 % Favored : 81.18 % 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: 1.35 (0.29), residues: 759 helix: 2.08 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -2.16 (0.32), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 79 TYR 0.011 0.002 TYR G 57 PHE 0.013 0.002 PHE A 78 TRP 0.008 0.002 TRP E 86 HIS 0.004 0.001 HIS E 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.22 (12379) covalent geometry : angle 0.72315 / 0.41 (17860) hydrogen bonds : bond 0.08354 / 5.60 ( 675) hydrogen bonds : angle 3.08493 / 2.19 ( 1724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.217 Fit side-chains REVERT: B 31 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7584 (tttp) REVERT: H 86 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.8027 (mpt90) REVERT: H 108 LYS cc_start: 0.8470 (mtpp) cc_final: 0.8241 (mttt) outliers start: 19 outliers final: 11 residues processed: 125 average time/residue: 0.9230 time to fit residues: 120.8800 Evaluate side-chains 123 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain K residue 535 SER Chi-restraints excluded: chain L residue 515 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.149750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.099558 restraints weight = 16104.471| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.42 r_work: 0.3145 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12379 Z= 0.182 Angle : 0.677 8.833 17860 Z= 0.386 Chirality : 0.047 0.288 2033 Planarity : 0.005 0.043 1328 Dihedral : 30.734 178.985 3885 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.95 % Allowed : 16.49 % Favored : 80.56 % 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: 1.67 (0.29), residues: 759 helix: 2.30 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.99 (0.33), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 86 TYR 0.009 0.002 TYR C 50 PHE 0.011 0.002 PHE A 78 TRP 0.006 0.001 TRP E 47 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (12379) covalent geometry : angle 0.67681 / 0.39 (17860) hydrogen bonds : bond 0.07344 / 4.92 ( 675) hydrogen bonds : angle 2.97325 / 2.10 ( 1724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.337 Fit side-chains REVERT: B 31 LYS cc_start: 0.7905 (ttmm) cc_final: 0.7544 (tttp) REVERT: C 73 ASN cc_start: 0.8673 (t0) cc_final: 0.8461 (t0) REVERT: H 108 LYS cc_start: 0.8415 (mtpp) cc_final: 0.8185 (mttt) outliers start: 19 outliers final: 13 residues processed: 124 average time/residue: 0.8913 time to fit residues: 115.9422 Evaluate side-chains 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain K residue 535 SER Chi-restraints excluded: chain L residue 515 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 72 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.151134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.101912 restraints weight = 16128.838| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.38 r_work: 0.3180 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 12379 Z= 0.144 Angle : 0.637 8.238 17860 Z= 0.369 Chirality : 0.045 0.287 2033 Planarity : 0.004 0.056 1328 Dihedral : 30.701 179.003 3885 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.64 % Allowed : 18.04 % Favored : 79.32 % 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: 2.06 (0.30), residues: 759 helix: 2.59 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.84 (0.34), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.012 0.001 TYR B 51 PHE 0.008 0.001 PHE F 61 TRP 0.004 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (12379) covalent geometry : angle 0.63661 / 0.37 (17860) hydrogen bonds : bond 0.06485 / 4.35 ( 675) hydrogen bonds : angle 2.88773 / 2.04 ( 1724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.268 Fit side-chains REVERT: B 31 LYS cc_start: 0.7847 (ttmm) cc_final: 0.7491 (tttp) REVERT: C 73 ASN cc_start: 0.8639 (t0) cc_final: 0.8406 (t0) outliers start: 17 outliers final: 13 residues processed: 123 average time/residue: 0.9255 time to fit residues: 119.4220 Evaluate side-chains 123 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 535 SER Chi-restraints excluded: chain L residue 515 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 50.0000 chunk 31 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.154426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.106646 restraints weight = 16470.241| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.35 r_work: 0.3324 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12379 Z= 0.138 Angle : 0.611 7.758 17860 Z= 0.357 Chirality : 0.043 0.287 2033 Planarity : 0.004 0.039 1328 Dihedral : 30.659 179.169 3885 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.42 % Allowed : 16.95 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.33 (0.30), residues: 759 helix: 2.78 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.68 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 77 TYR 0.010 0.001 TYR F 51 PHE 0.009 0.001 PHE A 78 TRP 0.004 0.001 TRP E 47 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.14 (12379) covalent geometry : angle 0.61072 / 0.36 (17860) hydrogen bonds : bond 0.05948 / 3.99 ( 675) hydrogen bonds : angle 2.79304 / 1.97 ( 1724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.340 Fit side-chains REVERT: B 31 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7500 (tttp) REVERT: C 73 ASN cc_start: 0.8679 (t0) cc_final: 0.8416 (t0) REVERT: D 68 ASP cc_start: 0.8876 (t0) cc_final: 0.8566 (t0) outliers start: 22 outliers final: 11 residues processed: 128 average time/residue: 1.0152 time to fit residues: 136.1693 Evaluate side-chains 122 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 535 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 18 optimal weight: 0.0470 chunk 83 optimal weight: 50.0000 chunk 3 optimal weight: 1.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.153495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.105008 restraints weight = 16375.888| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.37 r_work: 0.3302 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12379 Z= 0.149 Angle : 0.625 7.909 17860 Z= 0.361 Chirality : 0.044 0.281 2033 Planarity : 0.004 0.039 1328 Dihedral : 30.652 179.406 3883 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.33 % Allowed : 18.97 % Favored : 78.69 % 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: 2.39 (0.30), residues: 759 helix: 2.81 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.63 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 77 TYR 0.007 0.001 TYR H 40 PHE 0.009 0.001 PHE A 78 TRP 0.004 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (12379) covalent geometry : angle 0.62516 / 0.36 (17860) hydrogen bonds : bond 0.06236 / 4.18 ( 675) hydrogen bonds : angle 2.78394 / 1.96 ( 1724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.213 Fit side-chains REVERT: B 31 LYS cc_start: 0.7877 (ttmm) cc_final: 0.7533 (tttp) REVERT: C 73 ASN cc_start: 0.8698 (t0) cc_final: 0.8422 (t0) REVERT: D 68 ASP cc_start: 0.8908 (t0) cc_final: 0.8604 (t0) outliers start: 15 outliers final: 11 residues processed: 122 average time/residue: 1.0059 time to fit residues: 128.3330 Evaluate side-chains 120 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 535 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.154086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.106063 restraints weight = 16423.885| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.35 r_work: 0.3312 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12379 Z= 0.148 Angle : 0.626 7.587 17860 Z= 0.362 Chirality : 0.043 0.274 2033 Planarity : 0.004 0.041 1328 Dihedral : 30.648 179.411 3883 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.49 % Allowed : 18.97 % Favored : 78.54 % 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: 2.44 (0.30), residues: 759 helix: 2.84 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.57 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 86 TYR 0.010 0.001 TYR F 51 PHE 0.009 0.001 PHE A 78 TRP 0.004 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.15 (12379) covalent geometry : angle 0.62620 / 0.36 (17860) hydrogen bonds : bond 0.06120 / 4.10 ( 675) hydrogen bonds : angle 2.76964 / 1.95 ( 1724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.353 Fit side-chains REVERT: B 31 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7501 (tttp) REVERT: C 73 ASN cc_start: 0.8742 (t0) cc_final: 0.8513 (t0) REVERT: D 68 ASP cc_start: 0.8906 (t0) cc_final: 0.8596 (t0) outliers start: 16 outliers final: 13 residues processed: 122 average time/residue: 0.9659 time to fit residues: 123.6730 Evaluate side-chains 122 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 535 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 0.0000 chunk 35 optimal weight: 0.8980 chunk 25 optimal weight: 0.0040 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 70 optimal weight: 50.0000 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.154206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.106062 restraints weight = 16282.183| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.35 r_work: 0.3318 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12379 Z= 0.137 Angle : 0.619 7.584 17860 Z= 0.358 Chirality : 0.043 0.274 2033 Planarity : 0.004 0.039 1328 Dihedral : 30.644 179.392 3883 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.18 % Allowed : 18.97 % Favored : 78.85 % 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: 2.52 (0.30), residues: 759 helix: 2.90 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.54 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 77 TYR 0.008 0.001 TYR H 40 PHE 0.009 0.001 PHE F 61 TRP 0.004 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.14 (12379) covalent geometry : angle 0.61911 / 0.36 (17860) hydrogen bonds : bond 0.05861 / 3.93 ( 675) hydrogen bonds : angle 2.77129 / 1.95 ( 1724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.212 Fit side-chains REVERT: B 31 LYS cc_start: 0.7833 (ttmm) cc_final: 0.7491 (tttp) REVERT: B 91 LYS cc_start: 0.8928 (tttp) cc_final: 0.8297 (ttpt) REVERT: C 73 ASN cc_start: 0.8725 (t0) cc_final: 0.8492 (t0) REVERT: D 68 ASP cc_start: 0.8882 (t0) cc_final: 0.8510 (t0) outliers start: 14 outliers final: 12 residues processed: 120 average time/residue: 0.9971 time to fit residues: 125.2389 Evaluate side-chains 122 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 535 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.153816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.105863 restraints weight = 16382.523| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.35 r_work: 0.3308 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12379 Z= 0.151 Angle : 0.632 7.670 17860 Z= 0.365 Chirality : 0.044 0.275 2033 Planarity : 0.004 0.041 1328 Dihedral : 30.640 179.573 3883 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.18 % Allowed : 19.13 % Favored : 78.69 % 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: 2.47 (0.30), residues: 759 helix: 2.85 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.53 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.008 0.001 TYR H 40 PHE 0.009 0.001 PHE A 78 TRP 0.004 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 (12379) covalent geometry : angle 0.63246 / 0.36 (17860) hydrogen bonds : bond 0.06195 / 4.15 ( 675) hydrogen bonds : angle 2.77507 / 1.96 ( 1724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.323 Fit side-chains REVERT: B 31 LYS cc_start: 0.7868 (ttmm) cc_final: 0.7532 (tttp) REVERT: C 73 ASN cc_start: 0.8779 (t0) cc_final: 0.8495 (t0) REVERT: D 68 ASP cc_start: 0.8903 (t0) cc_final: 0.8592 (t0) outliers start: 14 outliers final: 9 residues processed: 119 average time/residue: 1.0099 time to fit residues: 125.8590 Evaluate side-chains 119 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain K residue 535 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 11 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.0030 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 40.0000 chunk 78 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 overall best weight: 0.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.154336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.106322 restraints weight = 16410.543| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.34 r_work: 0.3317 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12379 Z= 0.136 Angle : 0.621 8.626 17860 Z= 0.358 Chirality : 0.043 0.275 2033 Planarity : 0.005 0.078 1328 Dihedral : 30.642 179.461 3883 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.56 % Allowed : 19.44 % Favored : 79.00 % 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: 2.57 (0.30), residues: 759 helix: 2.92 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.48 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 77 TYR 0.008 0.001 TYR H 40 PHE 0.009 0.001 PHE F 61 TRP 0.003 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.14 (12379) covalent geometry : angle 0.62148 / 0.36 (17860) hydrogen bonds : bond 0.05809 / 3.90 ( 675) hydrogen bonds : angle 2.77380 / 1.95 ( 1724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4666.37 seconds wall clock time: 79 minutes 52.73 seconds (4792.73 seconds total)