Starting phenix.real_space_refine on Wed Mar 4 06:07:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r5r_14334/03_2026/7r5r_14334.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r5r_14334/03_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_14334/03_2026/7r5r_14334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r5r_14334/03_2026/7r5r_14334.map" model { file = "/net/cci-nas-00/data/ceres_data/7r5r_14334/03_2026/7r5r_14334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r5r_14334/03_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-dev-5986/lib/python3.9/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: 2.69, per 1000 atoms: 0.23 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: 0.95 Conformation dependent library (CDL) restraints added in 347.8 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: 1.75 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: 2.24 Time building geometry restraints manager: 1.29 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 1.50e-02 4.44e+03 2.54e+01 bond pdb=" O3' DA I 17 " pdb=" P DT I 18 " ideal model delta sigma weight residual 1.607 1.548 0.059 1.50e-02 4.44e+03 1.57e+01 bond pdb=" C1' DG J 34 " pdb=" N9 DG J 34 " ideal model delta sigma weight residual 1.460 1.388 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1' DG I -20 " pdb=" N9 DG I -20 " ideal model delta sigma weight residual 1.460 1.394 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O3' DG J -16 " pdb=" P DT J -15 " ideal model delta sigma weight residual 1.607 1.654 -0.047 1.50e-02 4.44e+03 9.87e+00 ... (remaining 12374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 17797 3.19 - 6.37: 46 6.37 - 9.56: 12 9.56 - 12.74: 2 12.74 - 15.93: 3 Bond angle restraints: 17860 Sorted by residual: angle pdb=" C4' DA J -18 " pdb=" C3' DA J -18 " pdb=" O3' DA J -18 " ideal model delta sigma weight residual 110.00 94.07 15.93 1.50e+00 4.44e-01 1.13e+02 angle pdb=" C3' DA I 17 " pdb=" O3' DA I 17 " pdb=" P DT I 18 " ideal model delta sigma weight residual 120.20 134.92 -14.72 1.50e+00 4.44e-01 9.64e+01 angle pdb=" O3' DT I 18 " pdb=" C3' DT I 18 " pdb=" C2' DT I 18 " ideal model delta sigma weight residual 111.50 98.04 13.46 1.50e+00 4.44e-01 8.05e+01 angle pdb=" O3' DA J -18 " pdb=" C3' DA J -18 " pdb=" C2' DA J -18 " ideal model delta sigma weight residual 111.50 100.12 11.38 1.50e+00 4.44e-01 5.76e+01 angle pdb=" C4' DT I 18 " pdb=" C3' DT I 18 " pdb=" O3' DT I 18 " ideal model delta sigma weight residual 110.00 99.69 10.31 1.50e+00 4.44e-01 4.73e+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 - 0.098: 1975 0.098 - 0.196: 47 0.196 - 0.295: 8 0.295 - 0.393: 2 0.393 - 0.491: 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 -2.66 -3.15 0.49 2.00e-01 2.50e+01 6.03e+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 -2.66 -3.04 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C3' DT J -15 " pdb=" C4' DT J -15 " pdb=" O3' DT J -15 " pdb=" C2' DT J -15 " both_signs ideal model delta sigma weight residual False -2.66 -2.96 0.30 2.00e-01 2.50e+01 2.22e+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: 4.460 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.170 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:8.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3787 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 : 0.004 0.076 12379 Z= 0.184 Angle : 0.656 15.927 17860 Z= 0.422 Chirality : 0.040 0.491 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 covalent geometry : bond 0.00364 (12379) covalent geometry : angle 0.65580 (17860) hydrogen bonds : bond 0.10583 ( 675) hydrogen bonds : angle 3.56051 ( 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: D 86 ARG cc_start: 0.6545 (mmt-90) cc_final: 0.6246 (mmt90) REVERT: F 44 LYS cc_start: 0.5833 (tttt) cc_final: 0.5629 (tttm) 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: 0.6762 (mmm-85) REVERT: H 86 ARG cc_start: 0.6084 (mmt90) cc_final: 0.5810 (mpt-90) outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 1.1840 time to fit residues: 165.3410 Evaluate side-chains 114 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 45 optimal weight: 3.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4066 r_free = 0.4066 target = 0.154004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.105355 restraints weight = 16213.644| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.38 r_work: 0.3240 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12379 Z= 0.157 Angle : 0.563 6.969 17860 Z= 0.338 Chirality : 0.033 0.130 2033 Planarity : 0.004 0.037 1328 Dihedral : 30.202 179.204 3885 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.18 % Allowed : 16.02 % Favored : 81.80 % 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: 1.49 (0.29), residues: 759 helix: 2.24 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -2.25 (0.32), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 77 TYR 0.010 0.001 TYR B 51 PHE 0.006 0.001 PHE F 61 TRP 0.003 0.001 TRP E 47 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00331 (12379) covalent geometry : angle 0.56305 (17860) hydrogen bonds : bond 0.05361 ( 675) hydrogen bonds : angle 2.67922 ( 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 130 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.362 Fit side-chains REVERT: B 31 LYS cc_start: 0.7806 (ttmm) cc_final: 0.7445 (tttp) REVERT: B 91 LYS cc_start: 0.8985 (ttmm) cc_final: 0.8269 (ttpt) REVERT: D 68 ASP cc_start: 0.8841 (t0) cc_final: 0.8426 (t0) REVERT: D 86 ARG cc_start: 0.8370 (mmt-90) cc_final: 0.8128 (mmt90) outliers start: 14 outliers final: 6 residues processed: 126 average time/residue: 1.1108 time to fit residues: 146.2903 Evaluate side-chains 112 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 46 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain K residue 535 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.0980 chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 18 optimal weight: 0.0010 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.155194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.107974 restraints weight = 16563.659| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.40 r_work: 0.3336 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12379 Z= 0.159 Angle : 0.562 7.111 17860 Z= 0.337 Chirality : 0.033 0.127 2033 Planarity : 0.004 0.038 1328 Dihedral : 30.233 178.962 3883 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.02 % Allowed : 16.95 % Favored : 81.03 % 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: 2.08 (0.30), residues: 759 helix: 2.63 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 86 TYR 0.009 0.001 TYR B 51 PHE 0.006 0.001 PHE H 70 TRP 0.003 0.001 TRP E 47 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00336 (12379) covalent geometry : angle 0.56193 (17860) hydrogen bonds : bond 0.05497 ( 675) hydrogen bonds : angle 2.65670 ( 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 129 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.321 Fit side-chains REVERT: B 31 LYS cc_start: 0.7993 (ttmm) cc_final: 0.7627 (tttp) REVERT: B 91 LYS cc_start: 0.9021 (ttmm) cc_final: 0.8206 (ttpt) REVERT: D 68 ASP cc_start: 0.9061 (t0) cc_final: 0.8758 (t0) REVERT: D 86 ARG cc_start: 0.8495 (mmt-90) cc_final: 0.8218 (mmt90) outliers start: 13 outliers final: 7 residues processed: 124 average time/residue: 1.0886 time to fit residues: 141.0717 Evaluate side-chains 116 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 76 VAL Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 46 LYS 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: 0.5980 chunk 35 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.155598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.107974 restraints weight = 16511.677| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.37 r_work: 0.3341 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12379 Z= 0.151 Angle : 0.557 7.047 17860 Z= 0.334 Chirality : 0.033 0.127 2033 Planarity : 0.004 0.038 1328 Dihedral : 30.209 179.003 3883 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.33 % Allowed : 17.57 % Favored : 80.09 % 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: 2.38 (0.30), residues: 759 helix: 2.83 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.70 (0.34), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 77 TYR 0.009 0.001 TYR B 51 PHE 0.007 0.001 PHE F 61 TRP 0.003 0.001 TRP E 47 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00316 (12379) covalent geometry : angle 0.55707 (17860) hydrogen bonds : bond 0.05237 ( 675) hydrogen bonds : angle 2.62338 ( 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 130 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.360 Fit side-chains REVERT: B 31 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7503 (tttp) REVERT: B 91 LYS cc_start: 0.8968 (ttmm) cc_final: 0.8177 (ttpt) REVERT: D 68 ASP cc_start: 0.8864 (t0) cc_final: 0.8497 (t0) REVERT: D 86 ARG cc_start: 0.8431 (mmt-90) cc_final: 0.8165 (mmt90) outliers start: 15 outliers final: 11 residues processed: 125 average time/residue: 1.0395 time to fit residues: 136.0115 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 : 0.317 ------------------------------------------------------------------------------- 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 47 SER 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 F residue 63 GLU 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: 0.6980 chunk 42 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.153306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.105452 restraints weight = 16330.660| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.34 r_work: 0.3291 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12379 Z= 0.177 Angle : 0.588 7.963 17860 Z= 0.350 Chirality : 0.034 0.128 2033 Planarity : 0.004 0.039 1328 Dihedral : 30.272 178.661 3883 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.95 % Allowed : 17.26 % Favored : 79.78 % 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: 2.76 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.62 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.012 0.001 TYR B 51 PHE 0.009 0.001 PHE A 78 TRP 0.005 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00383 (12379) covalent geometry : angle 0.58829 (17860) hydrogen bonds : bond 0.06130 ( 675) hydrogen bonds : angle 2.74416 ( 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 138 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.253 Fit side-chains REVERT: B 31 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7662 (tttp) REVERT: B 91 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8240 (ttpt) REVERT: C 73 ASN cc_start: 0.8769 (t0) cc_final: 0.8503 (t0) REVERT: D 86 ARG cc_start: 0.8558 (mmt-90) cc_final: 0.8213 (mmt90) REVERT: F 52 GLU cc_start: 0.7723 (mp0) cc_final: 0.7466 (mm-30) outliers start: 19 outliers final: 13 residues processed: 130 average time/residue: 1.0587 time to fit residues: 143.7421 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 : 0.313 ------------------------------------------------------------------------------- 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 47 SER 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 F residue 46 ILE Chi-restraints excluded: chain F residue 63 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 50.0000 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.152388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104720 restraints weight = 16342.005| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.34 r_work: 0.3285 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12379 Z= 0.181 Angle : 0.596 7.721 17860 Z= 0.354 Chirality : 0.035 0.129 2033 Planarity : 0.004 0.043 1328 Dihedral : 30.281 178.092 3883 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.64 % Allowed : 17.73 % 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: 2.38 (0.30), residues: 759 helix: 2.78 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.56 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 77 TYR 0.008 0.001 TYR H 40 PHE 0.007 0.001 PHE H 70 TRP 0.005 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00395 (12379) covalent geometry : angle 0.59623 (17860) hydrogen bonds : bond 0.06166 ( 675) hydrogen bonds : angle 2.74185 ( 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 133 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.371 Fit side-chains REVERT: B 31 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7651 (tttp) REVERT: C 73 ASN cc_start: 0.8836 (t0) cc_final: 0.8581 (t0) REVERT: D 68 ASP cc_start: 0.9076 (t0) cc_final: 0.8721 (t0) REVERT: D 86 ARG cc_start: 0.8570 (mmt-90) cc_final: 0.8240 (mmt90) outliers start: 17 outliers final: 12 residues processed: 127 average time/residue: 1.0673 time to fit residues: 141.7991 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 : 0.343 ------------------------------------------------------------------------------- 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 47 SER 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 F residue 46 ILE Chi-restraints excluded: chain F residue 63 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 96 optimal weight: 0.0050 chunk 49 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 83 optimal weight: 50.0000 chunk 3 optimal weight: 0.9980 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.152745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.104787 restraints weight = 16289.453| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.34 r_work: 0.3290 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12379 Z= 0.166 Angle : 0.589 7.476 17860 Z= 0.351 Chirality : 0.034 0.130 2033 Planarity : 0.004 0.050 1328 Dihedral : 30.279 178.064 3883 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.18 % Allowed : 18.51 % 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: 2.45 (0.30), residues: 759 helix: 2.83 (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 0.006 0.000 ARG G 77 TYR 0.009 0.001 TYR B 51 PHE 0.007 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 covalent geometry : bond 0.00353 (12379) covalent geometry : angle 0.58916 (17860) hydrogen bonds : bond 0.05921 ( 675) hydrogen bonds : angle 2.73350 ( 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 124 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.323 Fit side-chains REVERT: B 31 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7542 (tttp) REVERT: C 73 ASN cc_start: 0.8782 (t0) cc_final: 0.8464 (t0) REVERT: D 68 ASP cc_start: 0.8903 (t0) cc_final: 0.8536 (t0) REVERT: D 86 ARG cc_start: 0.8499 (mmt-90) cc_final: 0.8165 (mmt90) REVERT: F 52 GLU cc_start: 0.7459 (mp0) cc_final: 0.7226 (mm-30) outliers start: 14 outliers final: 12 residues processed: 120 average time/residue: 1.0910 time to fit residues: 136.8243 Evaluate side-chains 121 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 47 SER 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 F residue 46 ILE Chi-restraints excluded: chain F residue 63 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.152015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.104893 restraints weight = 16336.082| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.34 r_work: 0.3287 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12379 Z= 0.184 Angle : 0.603 7.660 17860 Z= 0.357 Chirality : 0.035 0.129 2033 Planarity : 0.004 0.044 1328 Dihedral : 30.299 177.892 3883 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.18 % Allowed : 18.51 % 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: 2.40 (0.30), residues: 759 helix: 2.78 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.51 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.011 0.001 TYR B 51 PHE 0.008 0.002 PHE A 78 TRP 0.005 0.001 TRP E 47 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00403 (12379) covalent geometry : angle 0.60294 (17860) hydrogen bonds : bond 0.06267 ( 675) hydrogen bonds : angle 2.75067 ( 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 127 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.322 Fit side-chains REVERT: B 31 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7635 (tttp) REVERT: C 73 ASN cc_start: 0.8833 (t0) cc_final: 0.8578 (t0) REVERT: D 86 ARG cc_start: 0.8561 (mmt-90) cc_final: 0.8229 (mmt90) REVERT: F 52 GLU cc_start: 0.7690 (mp0) cc_final: 0.7404 (mm-30) outliers start: 14 outliers final: 13 residues processed: 123 average time/residue: 1.0177 time to fit residues: 130.8939 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 : 0.337 ------------------------------------------------------------------------------- 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 47 SER 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 F residue 46 ILE Chi-restraints excluded: chain F residue 63 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.152524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.104927 restraints weight = 16161.020| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.33 r_work: 0.3290 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12379 Z= 0.166 Angle : 0.598 8.565 17860 Z= 0.354 Chirality : 0.034 0.130 2033 Planarity : 0.004 0.046 1328 Dihedral : 30.297 177.882 3883 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.33 % Allowed : 18.35 % 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: 2.46 (0.30), residues: 759 helix: 2.83 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.49 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 42 TYR 0.010 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 covalent geometry : bond 0.00354 (12379) covalent geometry : angle 0.59790 (17860) hydrogen bonds : bond 0.05995 ( 675) hydrogen bonds : angle 2.75056 ( 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 125 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.315 Fit side-chains REVERT: B 31 LYS cc_start: 0.8002 (ttmm) cc_final: 0.7643 (tttp) REVERT: C 73 ASN cc_start: 0.8817 (t0) cc_final: 0.8549 (t0) REVERT: D 86 ARG cc_start: 0.8555 (mmt-90) cc_final: 0.8223 (mmt90) REVERT: F 52 GLU cc_start: 0.7650 (mp0) cc_final: 0.7394 (mm-30) outliers start: 15 outliers final: 13 residues processed: 121 average time/residue: 1.0292 time to fit residues: 130.2130 Evaluate side-chains 121 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 47 SER 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 F residue 46 ILE Chi-restraints excluded: chain F residue 63 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 98 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.0270 chunk 46 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.152921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.105336 restraints weight = 16377.699| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.34 r_work: 0.3298 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12379 Z= 0.156 Angle : 0.595 8.517 17860 Z= 0.352 Chirality : 0.034 0.130 2033 Planarity : 0.005 0.127 1328 Dihedral : 30.286 177.921 3883 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.18 % Allowed : 18.82 % 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: 2.56 (0.30), residues: 759 helix: 2.90 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.47 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 77 TYR 0.011 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 F 75 Details of bonding type rmsd covalent geometry : bond 0.00327 (12379) covalent geometry : angle 0.59492 (17860) hydrogen bonds : bond 0.05730 ( 675) hydrogen bonds : angle 2.73028 ( 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 124 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.330 Fit side-chains REVERT: B 31 LYS cc_start: 0.7968 (ttmm) cc_final: 0.7604 (tttp) REVERT: B 91 LYS cc_start: 0.8993 (tttp) cc_final: 0.8310 (ttpt) REVERT: C 73 ASN cc_start: 0.8806 (t0) cc_final: 0.8539 (t0) REVERT: D 86 ARG cc_start: 0.8542 (mmt-90) cc_final: 0.8209 (mmt90) REVERT: F 52 GLU cc_start: 0.7622 (mp0) cc_final: 0.7365 (mm-30) outliers start: 14 outliers final: 13 residues processed: 120 average time/residue: 0.9955 time to fit residues: 125.0819 Evaluate side-chains 121 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 47 SER 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 F residue 46 ILE Chi-restraints excluded: chain F residue 63 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.153441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.105356 restraints weight = 16420.664| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.37 r_work: 0.3303 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12379 Z= 0.155 Angle : 0.588 7.898 17860 Z= 0.350 Chirality : 0.033 0.130 2033 Planarity : 0.004 0.083 1328 Dihedral : 30.262 177.961 3883 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.33 % Allowed : 18.51 % Favored : 79.16 % 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: 2.60 (0.30), residues: 759 helix: 2.94 (0.21), residues: 533 sheet: None (None), residues: 0 loop : -1.46 (0.35), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 77 TYR 0.011 0.001 TYR B 51 PHE 0.008 0.001 PHE F 61 TRP 0.003 0.001 TRP E 47 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00322 (12379) covalent geometry : angle 0.58833 (17860) hydrogen bonds : bond 0.05528 ( 675) hydrogen bonds : angle 2.69231 ( 1724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5860.24 seconds wall clock time: 99 minutes 52.24 seconds (5992.24 seconds total)