Starting phenix.real_space_refine on Sun Jun 15 16:29:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tgg_25881/06_2025/7tgg_25881.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tgg_25881/06_2025/7tgg_25881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tgg_25881/06_2025/7tgg_25881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tgg_25881/06_2025/7tgg_25881.map" model { file = "/net/cci-nas-00/data/ceres_data/7tgg_25881/06_2025/7tgg_25881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tgg_25881/06_2025/7tgg_25881.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 11445 2.51 5 N 2985 2.21 5 O 3810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18255 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "a" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "B" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "C" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "D" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "E" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "F" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "G" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "H" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "I" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "J" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "K" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "L" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "M" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "N" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "O" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "P" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "Q" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "R" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "S" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "T" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "U" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "V" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "W" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "X" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "Y" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "Z" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "0" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "1" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "2" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 763 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Time building chain proxies: 10.16, per 1000 atoms: 0.56 Number of scatterers: 18255 At special positions: 0 Unit cell: (83.16, 83.16, 246.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 3810 8.00 N 2985 7.00 C 11445 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: 4.81 Conformation dependent library (CDL) restraints added in 2.9 seconds 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4530 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 27.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA A 31 " --> pdb=" O TYR A 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 55 removed outlier: 4.473A pdb=" N ALA B 31 " --> pdb=" O TYR B 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 45 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 55 removed outlier: 4.473A pdb=" N ALA D 31 " --> pdb=" O TYR D 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR D 45 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL F 10 " --> pdb=" O LEU F 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 11 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE F 15 " --> pdb=" O ALA F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA F 31 " --> pdb=" O TYR F 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR F 45 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL H 10 " --> pdb=" O LEU H 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA H 11 " --> pdb=" O LEU H 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE H 15 " --> pdb=" O ALA H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 55 removed outlier: 4.473A pdb=" N ALA H 31 " --> pdb=" O TYR H 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR H 45 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL J 10 " --> pdb=" O LEU J 6 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA J 11 " --> pdb=" O LEU J 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE J 15 " --> pdb=" O ALA J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA J 31 " --> pdb=" O TYR J 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR J 45 " --> pdb=" O ARG J 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL L 10 " --> pdb=" O LEU L 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE L 15 " --> pdb=" O ALA L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA L 31 " --> pdb=" O TYR L 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR L 45 " --> pdb=" O ARG L 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL N 10 " --> pdb=" O LEU N 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA N 11 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE N 15 " --> pdb=" O ALA N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 55 removed outlier: 4.473A pdb=" N ALA N 31 " --> pdb=" O TYR N 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL P 10 " --> pdb=" O LEU P 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE P 15 " --> pdb=" O ALA P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA P 31 " --> pdb=" O TYR P 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR P 45 " --> pdb=" O ARG P 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL R 10 " --> pdb=" O LEU R 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA R 11 " --> pdb=" O LEU R 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 55 removed outlier: 4.473A pdb=" N ALA R 31 " --> pdb=" O TYR R 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR R 45 " --> pdb=" O ARG R 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL T 10 " --> pdb=" O LEU T 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA T 31 " --> pdb=" O TYR T 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR T 45 " --> pdb=" O ARG T 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL V 10 " --> pdb=" O LEU V 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA V 11 " --> pdb=" O LEU V 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE V 15 " --> pdb=" O ALA V 11 " (cutoff:3.500A) Processing helix chain 'V' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA V 31 " --> pdb=" O TYR V 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR V 45 " --> pdb=" O ARG V 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL X 10 " --> pdb=" O LEU X 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA X 11 " --> pdb=" O LEU X 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE X 15 " --> pdb=" O ALA X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 55 removed outlier: 4.473A pdb=" N ALA X 31 " --> pdb=" O TYR X 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR X 45 " --> pdb=" O ARG X 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL Z 10 " --> pdb=" O LEU Z 6 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA Z 11 " --> pdb=" O LEU Z 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE Z 15 " --> pdb=" O ALA Z 11 " (cutoff:3.500A) Processing helix chain 'Z' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA Z 31 " --> pdb=" O TYR Z 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR Z 45 " --> pdb=" O ARG Z 41 " (cutoff:3.500A) Processing helix chain '1' and resid 4 through 17 removed outlier: 4.005A pdb=" N VAL 1 10 " --> pdb=" O LEU 1 6 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA 1 11 " --> pdb=" O LEU 1 7 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE 1 15 " --> pdb=" O ALA 1 11 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 55 removed outlier: 4.472A pdb=" N ALA 1 31 " --> pdb=" O TYR 1 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR 1 45 " --> pdb=" O ARG 1 41 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'a' and resid 22 through 28 Processing sheet with id=2, first strand: chain 'C' and resid 22 through 28 Processing sheet with id=3, first strand: chain 'E' and resid 22 through 28 Processing sheet with id=4, first strand: chain 'G' and resid 22 through 28 Processing sheet with id=5, first strand: chain 'I' and resid 22 through 28 Processing sheet with id=6, first strand: chain 'K' and resid 22 through 28 Processing sheet with id=7, first strand: chain 'M' and resid 22 through 28 Processing sheet with id=8, first strand: chain 'O' and resid 22 through 28 Processing sheet with id=9, first strand: chain 'Q' and resid 22 through 28 Processing sheet with id=10, first strand: chain 'S' and resid 22 through 28 Processing sheet with id=11, first strand: chain 'U' and resid 22 through 28 Processing sheet with id=12, first strand: chain 'W' and resid 22 through 28 Processing sheet with id=13, first strand: chain 'Y' and resid 22 through 28 Processing sheet with id=14, first strand: chain '0' and resid 22 through 28 Processing sheet with id=15, first strand: chain '2' and resid 22 through 28 660 hydrogen bonds defined for protein. 1935 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.52 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5880 1.34 - 1.46: 3411 1.46 - 1.57: 9264 1.57 - 1.69: 0 1.69 - 1.80: 30 Bond restraints: 18585 Sorted by residual: bond pdb=" CA THR K 15 " pdb=" CB THR K 15 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.58e-02 4.01e+03 2.00e+00 bond pdb=" CA THR W 15 " pdb=" CB THR W 15 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.58e-02 4.01e+03 1.96e+00 bond pdb=" CA THR 2 15 " pdb=" CB THR 2 15 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.58e-02 4.01e+03 1.94e+00 bond pdb=" CA THR E 15 " pdb=" CB THR E 15 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.58e-02 4.01e+03 1.93e+00 bond pdb=" CA THR O 15 " pdb=" CB THR O 15 " ideal model delta sigma weight residual 1.529 1.551 -0.022 1.58e-02 4.01e+03 1.93e+00 ... (remaining 18580 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 23739 1.35 - 2.69: 1342 2.69 - 4.04: 174 4.04 - 5.39: 65 5.39 - 6.73: 15 Bond angle restraints: 25335 Sorted by residual: angle pdb=" CA ASP Q 71 " pdb=" CB ASP Q 71 " pdb=" CG ASP Q 71 " ideal model delta sigma weight residual 112.60 115.10 -2.50 1.00e+00 1.00e+00 6.26e+00 angle pdb=" CA ASP I 71 " pdb=" CB ASP I 71 " pdb=" CG ASP I 71 " ideal model delta sigma weight residual 112.60 115.10 -2.50 1.00e+00 1.00e+00 6.23e+00 angle pdb=" CA ASP O 71 " pdb=" CB ASP O 71 " pdb=" CG ASP O 71 " ideal model delta sigma weight residual 112.60 115.09 -2.49 1.00e+00 1.00e+00 6.19e+00 angle pdb=" CA ASP a 71 " pdb=" CB ASP a 71 " pdb=" CG ASP a 71 " ideal model delta sigma weight residual 112.60 115.07 -2.47 1.00e+00 1.00e+00 6.11e+00 angle pdb=" CA ASP C 71 " pdb=" CB ASP C 71 " pdb=" CG ASP C 71 " ideal model delta sigma weight residual 112.60 115.07 -2.47 1.00e+00 1.00e+00 6.08e+00 ... (remaining 25330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 10125 15.36 - 30.72: 585 30.72 - 46.09: 135 46.09 - 61.45: 45 61.45 - 76.81: 15 Dihedral angle restraints: 10905 sinusoidal: 3870 harmonic: 7035 Sorted by residual: dihedral pdb=" CA PHE I 14 " pdb=" C PHE I 14 " pdb=" N THR I 15 " pdb=" CA THR I 15 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA PHE C 14 " pdb=" C PHE C 14 " pdb=" N THR C 15 " pdb=" CA THR C 15 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA PHE Y 14 " pdb=" C PHE Y 14 " pdb=" N THR Y 15 " pdb=" CA THR Y 15 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 10902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2028 0.038 - 0.077: 800 0.077 - 0.115: 127 0.115 - 0.154: 15 0.154 - 0.192: 45 Chirality restraints: 3015 Sorted by residual: chirality pdb=" CB ILE X 19 " pdb=" CA ILE X 19 " pdb=" CG1 ILE X 19 " pdb=" CG2 ILE X 19 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.22e-01 chirality pdb=" CB ILE R 19 " pdb=" CA ILE R 19 " pdb=" CG1 ILE R 19 " pdb=" CG2 ILE R 19 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" CB ILE J 19 " pdb=" CA ILE J 19 " pdb=" CG1 ILE J 19 " pdb=" CG2 ILE J 19 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.20e-01 ... (remaining 3012 not shown) Planarity restraints: 3225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP Q 73 " -0.016 2.00e-02 2.50e+03 1.24e-02 3.83e+00 pdb=" CG TRP Q 73 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP Q 73 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP Q 73 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP Q 73 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP Q 73 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP Q 73 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP Q 73 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP Q 73 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP Q 73 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 73 " 0.016 2.00e-02 2.50e+03 1.24e-02 3.82e+00 pdb=" CG TRP G 73 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP G 73 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP G 73 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 73 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 73 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 73 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 73 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 73 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP G 73 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 73 " 0.016 2.00e-02 2.50e+03 1.23e-02 3.81e+00 pdb=" CG TRP M 73 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP M 73 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP M 73 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP M 73 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP M 73 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP M 73 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 73 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 73 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP M 73 " 0.005 2.00e-02 2.50e+03 ... (remaining 3222 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 272 2.64 - 3.20: 19500 3.20 - 3.77: 28414 3.77 - 4.33: 39128 4.33 - 4.90: 62501 Nonbonded interactions: 149815 Sorted by model distance: nonbonded pdb=" OG1 THR O 15 " pdb=" NE2 GLN T 23 " model vdw 2.070 3.120 nonbonded pdb=" OG1 THR G 15 " pdb=" NE2 GLN L 23 " model vdw 2.070 3.120 nonbonded pdb=" OG1 THR K 15 " pdb=" NE2 GLN N 23 " model vdw 2.070 3.120 nonbonded pdb=" OG1 THR U 15 " pdb=" NE2 GLN Z 23 " model vdw 2.070 3.120 nonbonded pdb=" OG1 THR C 15 " pdb=" NE2 GLN H 23 " model vdw 2.070 3.120 ... (remaining 149810 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: 0.18 Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' } ncs_group { reference = chain '1' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 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: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 41.080 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 0.029 18585 Z= 0.178 Angle : 0.714 6.733 25335 Z= 0.413 Chirality : 0.045 0.192 3015 Planarity : 0.007 0.060 3225 Dihedral : 11.742 76.809 6375 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.16), residues: 2385 helix: -0.87 (0.19), residues: 675 sheet: 0.48 (0.20), residues: 285 loop : -2.31 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP Q 73 PHE 0.029 0.004 PHE B 24 TYR 0.011 0.002 TYR P 27 ARG 0.005 0.001 ARG V 28 Details of bonding type rmsd hydrogen bonds : bond 0.15122 ( 660) hydrogen bonds : angle 6.85141 ( 1935) covalent geometry : bond 0.00360 (18585) covalent geometry : angle 0.71375 (25335) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 1.925 Fit side-chains revert: symmetry clash REVERT: A 3 LEU cc_start: 0.8911 (tt) cc_final: 0.8202 (tt) REVERT: a 13 ASP cc_start: 0.8724 (m-30) cc_final: 0.8478 (t0) REVERT: a 101 TRP cc_start: 0.8632 (p-90) cc_final: 0.7701 (p-90) REVERT: C 101 TRP cc_start: 0.8368 (p-90) cc_final: 0.7501 (p-90) REVERT: D 3 LEU cc_start: 0.8893 (tt) cc_final: 0.8322 (tt) REVERT: E 13 ASP cc_start: 0.8660 (m-30) cc_final: 0.8456 (t0) REVERT: E 43 TYR cc_start: 0.9024 (p90) cc_final: 0.8704 (p90) REVERT: E 101 TRP cc_start: 0.8468 (p-90) cc_final: 0.7469 (p-90) REVERT: F 3 LEU cc_start: 0.8952 (tt) cc_final: 0.8243 (tp) REVERT: G 13 ASP cc_start: 0.8637 (m-30) cc_final: 0.8429 (t0) REVERT: G 101 TRP cc_start: 0.8547 (p-90) cc_final: 0.7353 (p-90) REVERT: H 3 LEU cc_start: 0.8951 (tt) cc_final: 0.8427 (tp) REVERT: I 43 TYR cc_start: 0.9062 (p90) cc_final: 0.8785 (p90) REVERT: I 101 TRP cc_start: 0.8416 (p-90) cc_final: 0.8207 (p-90) REVERT: K 13 ASP cc_start: 0.8723 (m-30) cc_final: 0.8516 (t0) REVERT: K 40 ASN cc_start: 0.6570 (m-40) cc_final: 0.5786 (m-40) REVERT: K 42 ASP cc_start: 0.8119 (m-30) cc_final: 0.7829 (t70) REVERT: K 101 TRP cc_start: 0.8476 (p-90) cc_final: 0.7831 (p-90) REVERT: L 3 LEU cc_start: 0.8908 (tt) cc_final: 0.8678 (tt) REVERT: M 101 TRP cc_start: 0.8383 (p-90) cc_final: 0.7434 (p-90) REVERT: N 3 LEU cc_start: 0.8901 (tt) cc_final: 0.8118 (tt) REVERT: P 3 LEU cc_start: 0.8863 (tt) cc_final: 0.8203 (tt) REVERT: Q 13 ASP cc_start: 0.8585 (m-30) cc_final: 0.8330 (t0) REVERT: Q 101 TRP cc_start: 0.8452 (p-90) cc_final: 0.8038 (p90) REVERT: R 3 LEU cc_start: 0.8887 (tt) cc_final: 0.8343 (tt) REVERT: R 5 GLU cc_start: 0.8757 (tt0) cc_final: 0.8491 (tp30) REVERT: S 101 TRP cc_start: 0.8474 (p-90) cc_final: 0.7631 (p-90) REVERT: T 3 LEU cc_start: 0.8803 (tt) cc_final: 0.8012 (tt) REVERT: T 5 GLU cc_start: 0.8888 (tt0) cc_final: 0.8677 (tp30) REVERT: U 13 ASP cc_start: 0.8684 (m-30) cc_final: 0.8347 (t0) REVERT: U 43 TYR cc_start: 0.9084 (p90) cc_final: 0.8577 (p90) REVERT: U 101 TRP cc_start: 0.8525 (p-90) cc_final: 0.7597 (p-90) REVERT: V 3 LEU cc_start: 0.8859 (tt) cc_final: 0.8230 (tt) REVERT: W 101 TRP cc_start: 0.8525 (p-90) cc_final: 0.7549 (p-90) REVERT: X 3 LEU cc_start: 0.8798 (tt) cc_final: 0.7867 (tp) REVERT: Y 40 ASN cc_start: 0.6363 (m-40) cc_final: 0.5660 (m-40) REVERT: Y 101 TRP cc_start: 0.8481 (p-90) cc_final: 0.8054 (p-90) REVERT: Z 3 LEU cc_start: 0.8788 (tt) cc_final: 0.8523 (tp) REVERT: 0 101 TRP cc_start: 0.8560 (p-90) cc_final: 0.8091 (p-90) REVERT: 1 3 LEU cc_start: 0.8835 (tt) cc_final: 0.8336 (tp) REVERT: 1 5 GLU cc_start: 0.8701 (tt0) cc_final: 0.8332 (tp30) REVERT: 2 101 TRP cc_start: 0.8492 (p-90) cc_final: 0.7616 (p-90) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.2942 time to fit residues: 168.0076 Evaluate side-chains 222 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 217 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.047454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.039928 restraints weight = 99973.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.041597 restraints weight = 54800.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.042794 restraints weight = 35067.746| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18585 Z= 0.192 Angle : 0.620 4.896 25335 Z= 0.348 Chirality : 0.044 0.152 3015 Planarity : 0.005 0.050 3225 Dihedral : 7.079 67.017 2565 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.18), residues: 2385 helix: 0.35 (0.21), residues: 675 sheet: -0.30 (0.23), residues: 375 loop : -1.73 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 73 PHE 0.020 0.002 PHE P 24 TYR 0.013 0.002 TYR K 43 ARG 0.005 0.001 ARG X 28 Details of bonding type rmsd hydrogen bonds : bond 0.05227 ( 660) hydrogen bonds : angle 4.86299 ( 1935) covalent geometry : bond 0.00417 (18585) covalent geometry : angle 0.61968 (25335) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 43 TYR cc_start: 0.9310 (p90) cc_final: 0.9055 (p90) REVERT: C 101 TRP cc_start: 0.8490 (p-90) cc_final: 0.7534 (p-90) REVERT: E 101 TRP cc_start: 0.8472 (p-90) cc_final: 0.7564 (p-90) REVERT: G 101 TRP cc_start: 0.8659 (p-90) cc_final: 0.7631 (p-90) REVERT: I 101 TRP cc_start: 0.8455 (p-90) cc_final: 0.8149 (p-90) REVERT: K 101 TRP cc_start: 0.8467 (p-90) cc_final: 0.7663 (p-90) REVERT: L 5 GLU cc_start: 0.9328 (mm-30) cc_final: 0.9101 (tp30) REVERT: M 43 TYR cc_start: 0.9241 (p90) cc_final: 0.8604 (p90) REVERT: N 5 GLU cc_start: 0.9359 (mm-30) cc_final: 0.9120 (tp30) REVERT: N 6 LEU cc_start: 0.9598 (mm) cc_final: 0.9381 (mm) REVERT: O 40 ASN cc_start: 0.7230 (m-40) cc_final: 0.6449 (m-40) REVERT: Q 43 TYR cc_start: 0.9308 (p90) cc_final: 0.9040 (p90) REVERT: Q 101 TRP cc_start: 0.8577 (p-90) cc_final: 0.8095 (p-90) REVERT: S 101 TRP cc_start: 0.8534 (p-90) cc_final: 0.7529 (p-90) REVERT: T 3 LEU cc_start: 0.8685 (tt) cc_final: 0.8462 (tt) REVERT: U 101 TRP cc_start: 0.8608 (p-90) cc_final: 0.7755 (p-90) REVERT: V 5 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8958 (tp30) REVERT: V 30 LYS cc_start: 0.9286 (mmtt) cc_final: 0.8682 (tmtt) REVERT: V 48 GLU cc_start: 0.9509 (tp30) cc_final: 0.9250 (mm-30) REVERT: W 43 TYR cc_start: 0.9236 (p90) cc_final: 0.8946 (p90) REVERT: W 101 TRP cc_start: 0.8619 (p-90) cc_final: 0.7793 (p-90) REVERT: Y 43 TYR cc_start: 0.9352 (p90) cc_final: 0.9137 (p90) REVERT: Y 101 TRP cc_start: 0.8656 (p-90) cc_final: 0.8255 (p-90) REVERT: Z 3 LEU cc_start: 0.8854 (tt) cc_final: 0.8635 (tp) REVERT: Z 30 LYS cc_start: 0.9271 (mmtt) cc_final: 0.8638 (tmtt) REVERT: 0 40 ASN cc_start: 0.7159 (m-40) cc_final: 0.6377 (m-40) REVERT: 0 101 TRP cc_start: 0.8571 (p-90) cc_final: 0.7959 (p-90) REVERT: 1 5 GLU cc_start: 0.8885 (tt0) cc_final: 0.8411 (tp30) REVERT: 1 30 LYS cc_start: 0.9305 (mmtt) cc_final: 0.8583 (tmtt) REVERT: 2 101 TRP cc_start: 0.8546 (p-90) cc_final: 0.7607 (p-90) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.3078 time to fit residues: 147.7848 Evaluate side-chains 199 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 194 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 228 optimal weight: 5.9990 chunk 204 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.041495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.034600 restraints weight = 105717.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.036048 restraints weight = 58186.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.037093 restraints weight = 37545.478| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18585 Z= 0.241 Angle : 0.643 5.640 25335 Z= 0.355 Chirality : 0.044 0.207 3015 Planarity : 0.004 0.040 3225 Dihedral : 6.998 66.192 2565 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.18), residues: 2385 helix: 1.14 (0.22), residues: 675 sheet: -0.61 (0.25), residues: 375 loop : -1.62 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 73 PHE 0.012 0.002 PHE U 27 TYR 0.015 0.002 TYR U 43 ARG 0.003 0.001 ARG X 28 Details of bonding type rmsd hydrogen bonds : bond 0.05012 ( 660) hydrogen bonds : angle 4.77643 ( 1935) covalent geometry : bond 0.00510 (18585) covalent geometry : angle 0.64292 (25335) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9297 (tp30) cc_final: 0.8973 (tp30) REVERT: a 13 ASP cc_start: 0.8599 (p0) cc_final: 0.8271 (p0) REVERT: a 101 TRP cc_start: 0.8636 (p-90) cc_final: 0.7661 (p-90) REVERT: C 101 TRP cc_start: 0.8707 (p-90) cc_final: 0.7738 (p-90) REVERT: E 13 ASP cc_start: 0.8705 (p0) cc_final: 0.8390 (p0) REVERT: E 101 TRP cc_start: 0.8639 (p-90) cc_final: 0.7734 (p-90) REVERT: G 13 ASP cc_start: 0.8674 (p0) cc_final: 0.8208 (p0) REVERT: I 43 TYR cc_start: 0.9272 (p90) cc_final: 0.8897 (p90) REVERT: I 101 TRP cc_start: 0.8656 (p-90) cc_final: 0.8248 (p-90) REVERT: K 13 ASP cc_start: 0.8872 (p0) cc_final: 0.8542 (p0) REVERT: K 101 TRP cc_start: 0.8654 (p-90) cc_final: 0.7706 (p-90) REVERT: N 5 GLU cc_start: 0.9335 (mm-30) cc_final: 0.9077 (tp30) REVERT: N 6 LEU cc_start: 0.9609 (mm) cc_final: 0.9352 (mm) REVERT: P 5 GLU cc_start: 0.9357 (tp30) cc_final: 0.9079 (tp30) REVERT: Q 13 ASP cc_start: 0.8845 (p0) cc_final: 0.8405 (p0) REVERT: Q 43 TYR cc_start: 0.9337 (p90) cc_final: 0.8867 (p90) REVERT: Q 101 TRP cc_start: 0.8700 (p-90) cc_final: 0.8088 (p-90) REVERT: S 101 TRP cc_start: 0.8735 (p-90) cc_final: 0.7656 (p-90) REVERT: T 3 LEU cc_start: 0.9133 (tt) cc_final: 0.8776 (tt) REVERT: U 13 ASP cc_start: 0.8789 (p0) cc_final: 0.8392 (p0) REVERT: V 5 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9113 (tp30) REVERT: V 30 LYS cc_start: 0.9374 (mmtt) cc_final: 0.8741 (tmtt) REVERT: W 101 TRP cc_start: 0.8699 (p-90) cc_final: 0.7892 (p-90) REVERT: X 3 LEU cc_start: 0.8917 (tt) cc_final: 0.8679 (tt) REVERT: X 30 LYS cc_start: 0.9367 (mmtt) cc_final: 0.8605 (tmtt) REVERT: Y 101 TRP cc_start: 0.8792 (p-90) cc_final: 0.8230 (p-90) REVERT: Z 3 LEU cc_start: 0.9185 (tt) cc_final: 0.8839 (tp) REVERT: Z 5 GLU cc_start: 0.9274 (tp30) cc_final: 0.8974 (tp30) REVERT: Z 30 LYS cc_start: 0.9326 (mmtt) cc_final: 0.8790 (tmtt) REVERT: 0 43 TYR cc_start: 0.9426 (p90) cc_final: 0.9046 (p90) REVERT: 0 101 TRP cc_start: 0.8777 (p-90) cc_final: 0.8092 (p-90) REVERT: 1 5 GLU cc_start: 0.8828 (tt0) cc_final: 0.8393 (tp30) REVERT: 1 30 LYS cc_start: 0.9386 (mmtt) cc_final: 0.8637 (tmtt) REVERT: 2 3 LYS cc_start: 0.8267 (ptpp) cc_final: 0.7989 (ptpp) REVERT: 2 43 TYR cc_start: 0.9292 (p90) cc_final: 0.8940 (p90) REVERT: 2 101 TRP cc_start: 0.8614 (p-90) cc_final: 0.7668 (p-90) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3355 time to fit residues: 126.2016 Evaluate side-chains 192 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 87 optimal weight: 6.9990 chunk 103 optimal weight: 0.0670 chunk 119 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.042350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.035616 restraints weight = 104638.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.037103 restraints weight = 55919.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.038179 restraints weight = 35420.916| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18585 Z= 0.137 Angle : 0.548 5.087 25335 Z= 0.301 Chirality : 0.043 0.162 3015 Planarity : 0.003 0.025 3225 Dihedral : 6.268 58.594 2565 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.18), residues: 2385 helix: 1.65 (0.22), residues: 675 sheet: -0.76 (0.25), residues: 375 loop : -1.46 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP U 73 PHE 0.009 0.001 PHE A 51 TYR 0.015 0.002 TYR C 43 ARG 0.002 0.000 ARG X 28 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 660) hydrogen bonds : angle 4.44058 ( 1935) covalent geometry : bond 0.00295 (18585) covalent geometry : angle 0.54837 (25335) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9267 (tp30) cc_final: 0.8872 (tp30) REVERT: a 13 ASP cc_start: 0.8684 (p0) cc_final: 0.8377 (p0) REVERT: C 3 LYS cc_start: 0.8354 (ptpp) cc_final: 0.8119 (mptt) REVERT: C 43 TYR cc_start: 0.9417 (p90) cc_final: 0.9194 (p90) REVERT: C 101 TRP cc_start: 0.8566 (p-90) cc_final: 0.7642 (p-90) REVERT: E 13 ASP cc_start: 0.8770 (p0) cc_final: 0.8444 (p0) REVERT: G 13 ASP cc_start: 0.8722 (p0) cc_final: 0.8260 (p0) REVERT: G 101 TRP cc_start: 0.8616 (p-90) cc_final: 0.7562 (p-90) REVERT: I 43 TYR cc_start: 0.9224 (p90) cc_final: 0.8880 (p90) REVERT: I 101 TRP cc_start: 0.8510 (p-90) cc_final: 0.8164 (p-90) REVERT: K 13 ASP cc_start: 0.8912 (p0) cc_final: 0.8568 (p0) REVERT: K 43 TYR cc_start: 0.9369 (p90) cc_final: 0.9015 (p90) REVERT: K 101 TRP cc_start: 0.8460 (p-90) cc_final: 0.7591 (p-90) REVERT: L 5 GLU cc_start: 0.9320 (mm-30) cc_final: 0.9003 (tp30) REVERT: N 5 GLU cc_start: 0.9358 (mm-30) cc_final: 0.8996 (tp30) REVERT: N 6 LEU cc_start: 0.9606 (mm) cc_final: 0.9319 (mm) REVERT: Q 13 ASP cc_start: 0.8886 (p0) cc_final: 0.8425 (p0) REVERT: Q 101 TRP cc_start: 0.8570 (p-90) cc_final: 0.8048 (p-90) REVERT: R 6 LEU cc_start: 0.9756 (mm) cc_final: 0.9524 (mm) REVERT: S 43 TYR cc_start: 0.9398 (p90) cc_final: 0.8816 (p90) REVERT: S 101 TRP cc_start: 0.8557 (p-90) cc_final: 0.7517 (p-90) REVERT: U 13 ASP cc_start: 0.8823 (p0) cc_final: 0.8435 (p0) REVERT: V 5 GLU cc_start: 0.9344 (mm-30) cc_final: 0.9075 (tp30) REVERT: V 30 LYS cc_start: 0.9367 (mmtt) cc_final: 0.8743 (tmtt) REVERT: W 48 LYS cc_start: 0.9057 (ttpp) cc_final: 0.8755 (ttmm) REVERT: W 101 TRP cc_start: 0.8531 (p-90) cc_final: 0.7737 (p-90) REVERT: X 3 LEU cc_start: 0.8978 (tt) cc_final: 0.8693 (tt) REVERT: X 6 LEU cc_start: 0.9784 (mm) cc_final: 0.9567 (mm) REVERT: X 30 LYS cc_start: 0.9344 (mmtt) cc_final: 0.8608 (tmtt) REVERT: Y 13 ASP cc_start: 0.8646 (p0) cc_final: 0.8336 (p0) REVERT: Y 101 TRP cc_start: 0.8644 (p-90) cc_final: 0.8219 (p-90) REVERT: Z 5 GLU cc_start: 0.9278 (tp30) cc_final: 0.9051 (tp30) REVERT: Z 30 LYS cc_start: 0.9358 (mmtt) cc_final: 0.8835 (tmtt) REVERT: 0 101 TRP cc_start: 0.8645 (p-90) cc_final: 0.8150 (p-90) REVERT: 1 5 GLU cc_start: 0.8793 (tt0) cc_final: 0.8320 (tp30) REVERT: 1 30 LYS cc_start: 0.9386 (mmtt) cc_final: 0.8654 (tmtt) REVERT: 2 43 TYR cc_start: 0.9033 (p90) cc_final: 0.8751 (p90) REVERT: 2 48 LYS cc_start: 0.9122 (ttpp) cc_final: 0.8782 (ttmm) REVERT: 2 101 TRP cc_start: 0.8594 (p-90) cc_final: 0.7680 (p-90) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3542 time to fit residues: 136.3511 Evaluate side-chains 180 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 3.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 55 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 9 optimal weight: 0.0040 chunk 127 optimal weight: 10.0000 chunk 194 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** T 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.043131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.036273 restraints weight = 103741.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.037806 restraints weight = 54721.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.038895 restraints weight = 34247.248| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18585 Z= 0.112 Angle : 0.519 6.102 25335 Z= 0.284 Chirality : 0.042 0.177 3015 Planarity : 0.003 0.031 3225 Dihedral : 5.739 50.508 2565 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2385 helix: 2.05 (0.23), residues: 675 sheet: -0.69 (0.26), residues: 375 loop : -1.52 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 73 PHE 0.008 0.001 PHE A 51 TYR 0.014 0.001 TYR C 43 ARG 0.003 0.000 ARG T 41 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 660) hydrogen bonds : angle 4.28905 ( 1935) covalent geometry : bond 0.00235 (18585) covalent geometry : angle 0.51944 (25335) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9265 (tp30) cc_final: 0.8850 (tp30) REVERT: a 13 ASP cc_start: 0.8722 (p0) cc_final: 0.8411 (p0) REVERT: C 101 TRP cc_start: 0.8539 (p-90) cc_final: 0.7626 (p-90) REVERT: E 9 MET cc_start: 0.9303 (tpp) cc_final: 0.9102 (tpp) REVERT: E 13 ASP cc_start: 0.8771 (p0) cc_final: 0.8472 (p0) REVERT: G 13 ASP cc_start: 0.8746 (p0) cc_final: 0.8291 (p0) REVERT: G 101 TRP cc_start: 0.8531 (p-90) cc_final: 0.7528 (p-90) REVERT: I 101 TRP cc_start: 0.8505 (p-90) cc_final: 0.8133 (p-90) REVERT: K 13 ASP cc_start: 0.8913 (p0) cc_final: 0.8575 (p0) REVERT: K 43 TYR cc_start: 0.9281 (p90) cc_final: 0.8991 (p90) REVERT: K 48 LYS cc_start: 0.9027 (ttpp) cc_final: 0.8820 (ttmm) REVERT: K 101 TRP cc_start: 0.8345 (p-90) cc_final: 0.7457 (p-90) REVERT: L 5 GLU cc_start: 0.9345 (mm-30) cc_final: 0.9023 (tp30) REVERT: M 101 TRP cc_start: 0.8448 (p-90) cc_final: 0.7318 (p-90) REVERT: N 5 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8932 (tp30) REVERT: N 6 LEU cc_start: 0.9588 (mm) cc_final: 0.9324 (mm) REVERT: P 5 GLU cc_start: 0.9375 (tp30) cc_final: 0.9134 (tp30) REVERT: Q 13 ASP cc_start: 0.8841 (p0) cc_final: 0.8432 (p0) REVERT: Q 43 TYR cc_start: 0.9411 (p90) cc_final: 0.9199 (p90) REVERT: Q 101 TRP cc_start: 0.8481 (p-90) cc_final: 0.7970 (p-90) REVERT: S 43 TYR cc_start: 0.9315 (p90) cc_final: 0.8855 (p90) REVERT: S 101 TRP cc_start: 0.8507 (p-90) cc_final: 0.7395 (p-90) REVERT: U 13 ASP cc_start: 0.8857 (p0) cc_final: 0.8483 (p0) REVERT: V 5 GLU cc_start: 0.9345 (mm-30) cc_final: 0.9080 (tp30) REVERT: V 30 LYS cc_start: 0.9348 (mmtt) cc_final: 0.8753 (tmtt) REVERT: W 48 LYS cc_start: 0.8983 (ttpp) cc_final: 0.8765 (ttmm) REVERT: W 101 TRP cc_start: 0.8404 (p-90) cc_final: 0.7671 (p-90) REVERT: X 3 LEU cc_start: 0.9015 (tt) cc_final: 0.8710 (tt) REVERT: X 30 LYS cc_start: 0.9324 (mmtt) cc_final: 0.8634 (tmtt) REVERT: Y 13 ASP cc_start: 0.8670 (p0) cc_final: 0.8343 (p0) REVERT: Y 101 TRP cc_start: 0.8522 (p-90) cc_final: 0.8151 (p-90) REVERT: Z 5 GLU cc_start: 0.9319 (tp30) cc_final: 0.9020 (tp30) REVERT: Z 30 LYS cc_start: 0.9337 (mmtt) cc_final: 0.8815 (tmtt) REVERT: 0 101 TRP cc_start: 0.8552 (p-90) cc_final: 0.8023 (p-90) REVERT: 1 5 GLU cc_start: 0.8783 (tt0) cc_final: 0.8277 (tp30) REVERT: 1 30 LYS cc_start: 0.9347 (mmtt) cc_final: 0.8632 (tmtt) REVERT: 2 43 TYR cc_start: 0.9051 (p90) cc_final: 0.8762 (p90) REVERT: 2 48 LYS cc_start: 0.9103 (ttpp) cc_final: 0.8846 (ttmm) REVERT: 2 101 TRP cc_start: 0.8494 (p-90) cc_final: 0.7614 (p-90) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.3273 time to fit residues: 123.7622 Evaluate side-chains 180 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 83 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 206 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 213 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 73 optimal weight: 0.0970 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.044232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.037376 restraints weight = 102510.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.038930 restraints weight = 54413.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.040037 restraints weight = 34067.614| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 18585 Z= 0.104 Angle : 0.521 7.360 25335 Z= 0.279 Chirality : 0.042 0.171 3015 Planarity : 0.003 0.022 3225 Dihedral : 5.207 43.032 2565 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.93 % Favored : 91.03 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.18), residues: 2385 helix: 2.19 (0.23), residues: 675 sheet: -0.58 (0.26), residues: 375 loop : -1.61 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Q 73 PHE 0.011 0.001 PHE F 24 TYR 0.012 0.001 TYR K 43 ARG 0.002 0.000 ARG T 41 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 660) hydrogen bonds : angle 4.24632 ( 1935) covalent geometry : bond 0.00208 (18585) covalent geometry : angle 0.52121 (25335) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9278 (tp30) cc_final: 0.9006 (tp30) REVERT: a 13 ASP cc_start: 0.8749 (p0) cc_final: 0.8449 (p0) REVERT: a 101 TRP cc_start: 0.8526 (p-90) cc_final: 0.7556 (p-90) REVERT: C 101 TRP cc_start: 0.8424 (p-90) cc_final: 0.7434 (p-90) REVERT: D 6 LEU cc_start: 0.9590 (mm) cc_final: 0.9362 (mm) REVERT: E 9 MET cc_start: 0.9348 (tpp) cc_final: 0.9132 (tpp) REVERT: E 13 ASP cc_start: 0.8751 (p0) cc_final: 0.8444 (p0) REVERT: G 13 ASP cc_start: 0.8681 (p0) cc_final: 0.8244 (p0) REVERT: G 101 TRP cc_start: 0.8388 (p-90) cc_final: 0.7519 (p-90) REVERT: H 6 LEU cc_start: 0.9619 (mm) cc_final: 0.9417 (mm) REVERT: I 43 TYR cc_start: 0.9264 (p90) cc_final: 0.8896 (p90) REVERT: I 101 TRP cc_start: 0.8445 (p-90) cc_final: 0.8036 (p-90) REVERT: J 3 LEU cc_start: 0.9070 (tt) cc_final: 0.8855 (tt) REVERT: K 13 ASP cc_start: 0.8757 (p0) cc_final: 0.8436 (p0) REVERT: K 101 TRP cc_start: 0.8312 (p-90) cc_final: 0.7386 (p-90) REVERT: M 101 TRP cc_start: 0.8350 (p-90) cc_final: 0.7258 (p-90) REVERT: N 5 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8924 (tp30) REVERT: N 6 LEU cc_start: 0.9584 (mm) cc_final: 0.9308 (mm) REVERT: P 5 GLU cc_start: 0.9332 (tp30) cc_final: 0.9034 (tp30) REVERT: Q 13 ASP cc_start: 0.8882 (p0) cc_final: 0.8477 (p0) REVERT: Q 101 TRP cc_start: 0.8401 (p-90) cc_final: 0.7785 (p-90) REVERT: R 6 LEU cc_start: 0.9729 (mm) cc_final: 0.9500 (mm) REVERT: S 43 TYR cc_start: 0.9216 (p90) cc_final: 0.8924 (p90) REVERT: S 101 TRP cc_start: 0.8376 (p-90) cc_final: 0.7127 (p-90) REVERT: U 13 ASP cc_start: 0.8854 (p0) cc_final: 0.8496 (p0) REVERT: V 5 GLU cc_start: 0.9365 (mm-30) cc_final: 0.9046 (tp30) REVERT: V 30 LYS cc_start: 0.9307 (mmtt) cc_final: 0.8767 (tmtt) REVERT: W 101 TRP cc_start: 0.8331 (p-90) cc_final: 0.7709 (p-90) REVERT: X 3 LEU cc_start: 0.9029 (tt) cc_final: 0.8747 (tt) REVERT: X 30 LYS cc_start: 0.9285 (mmtt) cc_final: 0.8630 (tmtt) REVERT: Y 101 TRP cc_start: 0.8394 (p-90) cc_final: 0.8080 (p-90) REVERT: Z 30 LYS cc_start: 0.9311 (mmtt) cc_final: 0.8841 (tmtt) REVERT: 0 101 TRP cc_start: 0.8461 (p-90) cc_final: 0.7886 (p-90) REVERT: 1 5 GLU cc_start: 0.8751 (tt0) cc_final: 0.8214 (tp30) REVERT: 1 6 LEU cc_start: 0.9666 (mm) cc_final: 0.9459 (mm) REVERT: 1 30 LYS cc_start: 0.9338 (mmtt) cc_final: 0.8732 (tmtt) REVERT: 2 101 TRP cc_start: 0.8413 (p-90) cc_final: 0.7498 (p-90) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.2905 time to fit residues: 114.2309 Evaluate side-chains 176 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 183 optimal weight: 0.3980 chunk 176 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 179 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.042876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.036040 restraints weight = 103817.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.037549 restraints weight = 55673.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.038640 restraints weight = 35265.542| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18585 Z= 0.152 Angle : 0.551 6.688 25335 Z= 0.298 Chirality : 0.043 0.195 3015 Planarity : 0.003 0.044 3225 Dihedral : 5.314 43.648 2565 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 2385 helix: 2.34 (0.23), residues: 675 sheet: -0.63 (0.26), residues: 375 loop : -1.69 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 73 PHE 0.010 0.001 PHE J 51 TYR 0.021 0.001 TYR C 43 ARG 0.002 0.000 ARG P 41 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 660) hydrogen bonds : angle 4.33174 ( 1935) covalent geometry : bond 0.00331 (18585) covalent geometry : angle 0.55137 (25335) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9290 (tp30) cc_final: 0.8997 (tp30) REVERT: a 13 ASP cc_start: 0.8762 (p0) cc_final: 0.8465 (p0) REVERT: a 101 TRP cc_start: 0.8574 (p-90) cc_final: 0.7649 (p-90) REVERT: C 13 ASP cc_start: 0.8577 (p0) cc_final: 0.8272 (p0) REVERT: C 101 TRP cc_start: 0.8545 (p-90) cc_final: 0.7579 (p-90) REVERT: E 13 ASP cc_start: 0.8774 (p0) cc_final: 0.8456 (p0) REVERT: E 101 TRP cc_start: 0.8355 (p-90) cc_final: 0.7328 (p-90) REVERT: G 13 ASP cc_start: 0.8729 (p0) cc_final: 0.8313 (p0) REVERT: G 101 TRP cc_start: 0.8492 (p-90) cc_final: 0.7597 (p-90) REVERT: I 101 TRP cc_start: 0.8511 (p-90) cc_final: 0.8063 (p-90) REVERT: K 13 ASP cc_start: 0.8793 (p0) cc_final: 0.8473 (p0) REVERT: K 101 TRP cc_start: 0.8356 (p-90) cc_final: 0.7394 (p-90) REVERT: L 5 GLU cc_start: 0.9348 (mm-30) cc_final: 0.9065 (tp30) REVERT: M 13 ASP cc_start: 0.8629 (p0) cc_final: 0.8368 (p0) REVERT: M 101 TRP cc_start: 0.8432 (p-90) cc_final: 0.7363 (p-90) REVERT: N 5 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8903 (tp30) REVERT: N 6 LEU cc_start: 0.9577 (mm) cc_final: 0.9324 (mm) REVERT: O 13 ASP cc_start: 0.8518 (p0) cc_final: 0.8290 (p0) REVERT: P 5 GLU cc_start: 0.9327 (tp30) cc_final: 0.9004 (tp30) REVERT: Q 13 ASP cc_start: 0.8908 (p0) cc_final: 0.8581 (p0) REVERT: Q 101 TRP cc_start: 0.8491 (p-90) cc_final: 0.7840 (p-90) REVERT: R 6 LEU cc_start: 0.9708 (mm) cc_final: 0.9464 (mm) REVERT: S 43 TYR cc_start: 0.9352 (p90) cc_final: 0.9027 (p90) REVERT: S 101 TRP cc_start: 0.8438 (p-90) cc_final: 0.7234 (p-90) REVERT: U 13 ASP cc_start: 0.8818 (p0) cc_final: 0.8447 (p0) REVERT: V 5 GLU cc_start: 0.9350 (mm-30) cc_final: 0.9038 (tp30) REVERT: V 30 LYS cc_start: 0.9343 (mmtt) cc_final: 0.8847 (tmtt) REVERT: W 13 ASP cc_start: 0.8676 (p0) cc_final: 0.8433 (p0) REVERT: W 101 TRP cc_start: 0.8478 (p-90) cc_final: 0.7820 (p-90) REVERT: X 3 LEU cc_start: 0.9150 (tt) cc_final: 0.8885 (tt) REVERT: X 30 LYS cc_start: 0.9305 (mmtt) cc_final: 0.8661 (tmtt) REVERT: Y 101 TRP cc_start: 0.8469 (p-90) cc_final: 0.8124 (p-90) REVERT: Z 5 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8897 (tp30) REVERT: Z 30 LYS cc_start: 0.9326 (mmtt) cc_final: 0.8840 (tmtt) REVERT: 0 101 TRP cc_start: 0.8558 (p-90) cc_final: 0.7930 (p-90) REVERT: 1 5 GLU cc_start: 0.8758 (tt0) cc_final: 0.8293 (tp30) REVERT: 1 30 LYS cc_start: 0.9394 (mmtt) cc_final: 0.8734 (tmtt) REVERT: 2 101 TRP cc_start: 0.8493 (p-90) cc_final: 0.7538 (p-90) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2979 time to fit residues: 105.7632 Evaluate side-chains 166 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 220 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 0.0970 chunk 164 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.043468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.036793 restraints weight = 101124.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.038307 restraints weight = 54365.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.039388 restraints weight = 34402.764| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18585 Z= 0.113 Angle : 0.556 6.777 25335 Z= 0.293 Chirality : 0.044 0.190 3015 Planarity : 0.003 0.026 3225 Dihedral : 5.099 40.715 2565 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.18), residues: 2385 helix: 2.30 (0.22), residues: 675 sheet: -0.67 (0.26), residues: 375 loop : -1.75 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 73 PHE 0.008 0.001 PHE D 51 TYR 0.021 0.002 TYR I 43 ARG 0.002 0.000 ARG P 41 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 660) hydrogen bonds : angle 4.23435 ( 1935) covalent geometry : bond 0.00237 (18585) covalent geometry : angle 0.55647 (25335) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9269 (tp30) cc_final: 0.8955 (tp30) REVERT: a 13 ASP cc_start: 0.8764 (p0) cc_final: 0.8468 (p0) REVERT: a 101 TRP cc_start: 0.8457 (p-90) cc_final: 0.7580 (p-90) REVERT: C 13 ASP cc_start: 0.8568 (p0) cc_final: 0.8282 (p0) REVERT: C 101 TRP cc_start: 0.8451 (p-90) cc_final: 0.7469 (p-90) REVERT: E 13 ASP cc_start: 0.8768 (p0) cc_final: 0.8444 (p0) REVERT: E 101 TRP cc_start: 0.8218 (p-90) cc_final: 0.7290 (p-90) REVERT: G 13 ASP cc_start: 0.8705 (p0) cc_final: 0.8316 (p0) REVERT: G 101 TRP cc_start: 0.8328 (p-90) cc_final: 0.7515 (p-90) REVERT: H 6 LEU cc_start: 0.9606 (mm) cc_final: 0.9397 (mm) REVERT: I 101 TRP cc_start: 0.8391 (p-90) cc_final: 0.7984 (p-90) REVERT: K 13 ASP cc_start: 0.8761 (p0) cc_final: 0.8440 (p0) REVERT: K 43 TYR cc_start: 0.9344 (p90) cc_final: 0.9096 (p90) REVERT: K 101 TRP cc_start: 0.8317 (p-90) cc_final: 0.7297 (p-90) REVERT: L 5 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9104 (tp30) REVERT: M 13 ASP cc_start: 0.8639 (p0) cc_final: 0.8365 (p0) REVERT: M 101 TRP cc_start: 0.8290 (p-90) cc_final: 0.7309 (p-90) REVERT: N 5 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8718 (pt0) REVERT: O 13 ASP cc_start: 0.8538 (p0) cc_final: 0.8291 (p0) REVERT: P 5 GLU cc_start: 0.9300 (tp30) cc_final: 0.8986 (tp30) REVERT: Q 13 ASP cc_start: 0.8870 (p0) cc_final: 0.8551 (p0) REVERT: Q 101 TRP cc_start: 0.8358 (p-90) cc_final: 0.7756 (p-90) REVERT: R 6 LEU cc_start: 0.9715 (mm) cc_final: 0.9478 (mm) REVERT: S 43 TYR cc_start: 0.9269 (p90) cc_final: 0.9044 (p90) REVERT: S 101 TRP cc_start: 0.8303 (p-90) cc_final: 0.7261 (p-90) REVERT: U 13 ASP cc_start: 0.8808 (p0) cc_final: 0.8470 (p0) REVERT: V 5 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8984 (tp30) REVERT: V 30 LYS cc_start: 0.9350 (mmtt) cc_final: 0.8855 (tmtt) REVERT: W 13 ASP cc_start: 0.8693 (p0) cc_final: 0.8447 (p0) REVERT: W 101 TRP cc_start: 0.8326 (p-90) cc_final: 0.7760 (p-90) REVERT: X 3 LEU cc_start: 0.9152 (tt) cc_final: 0.8885 (tt) REVERT: X 30 LYS cc_start: 0.9286 (mmtt) cc_final: 0.8660 (tmtt) REVERT: Y 9 MET cc_start: 0.9516 (tpp) cc_final: 0.9293 (tpt) REVERT: Y 101 TRP cc_start: 0.8329 (p-90) cc_final: 0.8059 (p-90) REVERT: Z 30 LYS cc_start: 0.9304 (mmtt) cc_final: 0.8840 (tmtt) REVERT: 0 101 TRP cc_start: 0.8416 (p-90) cc_final: 0.7828 (p-90) REVERT: 1 5 GLU cc_start: 0.8783 (tt0) cc_final: 0.8251 (tp30) REVERT: 1 30 LYS cc_start: 0.9394 (mmtt) cc_final: 0.8744 (tmtt) REVERT: 2 101 TRP cc_start: 0.8392 (p-90) cc_final: 0.7518 (p-90) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.3049 time to fit residues: 110.7261 Evaluate side-chains 169 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 3.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 99 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 151 optimal weight: 0.0570 chunk 132 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 237 optimal weight: 0.6980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.043944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.037234 restraints weight = 100654.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.038778 restraints weight = 53707.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.039855 restraints weight = 33724.247| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18585 Z= 0.110 Angle : 0.560 8.411 25335 Z= 0.294 Chirality : 0.044 0.184 3015 Planarity : 0.003 0.027 3225 Dihedral : 4.946 38.301 2565 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.18), residues: 2385 helix: 2.30 (0.22), residues: 675 sheet: -0.68 (0.26), residues: 375 loop : -1.83 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 73 PHE 0.007 0.001 PHE C 14 TYR 0.024 0.001 TYR C 43 ARG 0.002 0.000 ARG W 54 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 660) hydrogen bonds : angle 4.18794 ( 1935) covalent geometry : bond 0.00227 (18585) covalent geometry : angle 0.56001 (25335) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9254 (tp30) cc_final: 0.8935 (tp30) REVERT: a 13 ASP cc_start: 0.8723 (p0) cc_final: 0.8443 (p0) REVERT: a 101 TRP cc_start: 0.8397 (p-90) cc_final: 0.7592 (p-90) REVERT: C 9 MET cc_start: 0.9466 (tpp) cc_final: 0.9220 (tpt) REVERT: C 13 ASP cc_start: 0.8697 (p0) cc_final: 0.8420 (p0) REVERT: C 101 TRP cc_start: 0.8343 (p-90) cc_final: 0.7350 (p-90) REVERT: E 13 ASP cc_start: 0.8761 (p0) cc_final: 0.8434 (p0) REVERT: E 101 TRP cc_start: 0.8147 (p-90) cc_final: 0.7283 (p-90) REVERT: G 13 ASP cc_start: 0.8719 (p0) cc_final: 0.8358 (p0) REVERT: G 101 TRP cc_start: 0.8248 (p-90) cc_final: 0.7528 (p-90) REVERT: H 6 LEU cc_start: 0.9592 (mm) cc_final: 0.9369 (mm) REVERT: I 101 TRP cc_start: 0.8295 (p-90) cc_final: 0.7863 (p-90) REVERT: K 13 ASP cc_start: 0.8750 (p0) cc_final: 0.8422 (p0) REVERT: K 101 TRP cc_start: 0.8206 (p-90) cc_final: 0.7141 (p-90) REVERT: L 5 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9056 (tp30) REVERT: M 13 ASP cc_start: 0.8672 (p0) cc_final: 0.8389 (p0) REVERT: M 101 TRP cc_start: 0.8282 (p-90) cc_final: 0.7374 (p-90) REVERT: N 5 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8693 (pt0) REVERT: O 13 ASP cc_start: 0.8585 (p0) cc_final: 0.8330 (p0) REVERT: P 5 GLU cc_start: 0.9280 (tp30) cc_final: 0.8924 (tp30) REVERT: Q 13 ASP cc_start: 0.8814 (p0) cc_final: 0.8448 (p0) REVERT: Q 101 TRP cc_start: 0.8270 (p-90) cc_final: 0.7652 (p-90) REVERT: R 6 LEU cc_start: 0.9706 (mm) cc_final: 0.9465 (mm) REVERT: S 26 TYR cc_start: 0.9319 (t80) cc_final: 0.9113 (t80) REVERT: S 101 TRP cc_start: 0.8267 (p-90) cc_final: 0.7254 (p-90) REVERT: U 13 ASP cc_start: 0.8806 (p0) cc_final: 0.8475 (p0) REVERT: V 5 GLU cc_start: 0.9308 (mm-30) cc_final: 0.8938 (tp30) REVERT: V 30 LYS cc_start: 0.9360 (mmtt) cc_final: 0.8862 (tmtt) REVERT: W 13 ASP cc_start: 0.8745 (p0) cc_final: 0.8489 (p0) REVERT: W 101 TRP cc_start: 0.8236 (p-90) cc_final: 0.7668 (p-90) REVERT: X 3 LEU cc_start: 0.9185 (tt) cc_final: 0.8905 (tt) REVERT: X 30 LYS cc_start: 0.9253 (mmtt) cc_final: 0.8644 (tmtt) REVERT: Y 9 MET cc_start: 0.9544 (tpp) cc_final: 0.9335 (tpt) REVERT: Y 101 TRP cc_start: 0.8244 (p-90) cc_final: 0.7973 (p-90) REVERT: Z 5 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8955 (tp30) REVERT: Z 30 LYS cc_start: 0.9286 (mmtt) cc_final: 0.8830 (tmtt) REVERT: 0 101 TRP cc_start: 0.8346 (p-90) cc_final: 0.7762 (p-90) REVERT: 1 6 LEU cc_start: 0.9631 (mm) cc_final: 0.9416 (mm) REVERT: 1 30 LYS cc_start: 0.9371 (mmtt) cc_final: 0.8759 (tmtt) REVERT: 2 26 TYR cc_start: 0.9291 (t80) cc_final: 0.9044 (t80) REVERT: 2 43 TYR cc_start: 0.8902 (p90) cc_final: 0.8666 (p90) REVERT: 2 101 TRP cc_start: 0.8311 (p-90) cc_final: 0.7419 (p-90) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.3009 time to fit residues: 110.4751 Evaluate side-chains 160 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 238 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 38 optimal weight: 0.0020 chunk 99 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.043611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.036859 restraints weight = 101418.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.038399 restraints weight = 53653.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.039474 restraints weight = 33671.688| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18585 Z= 0.117 Angle : 0.552 6.782 25335 Z= 0.292 Chirality : 0.044 0.186 3015 Planarity : 0.003 0.027 3225 Dihedral : 4.911 38.468 2565 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.18), residues: 2385 helix: 2.37 (0.22), residues: 675 sheet: -0.71 (0.26), residues: 375 loop : -1.86 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 73 PHE 0.007 0.001 PHE D 51 TYR 0.020 0.001 TYR I 43 ARG 0.002 0.000 ARG W 54 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 660) hydrogen bonds : angle 4.20675 ( 1935) covalent geometry : bond 0.00247 (18585) covalent geometry : angle 0.55198 (25335) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4770 Ramachandran restraints generated. 2385 Oldfield, 0 Emsley, 2385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.9314 (tp30) cc_final: 0.8998 (tp30) REVERT: a 13 ASP cc_start: 0.8828 (p0) cc_final: 0.8564 (p0) REVERT: a 101 TRP cc_start: 0.8559 (p-90) cc_final: 0.7682 (p-90) REVERT: C 9 MET cc_start: 0.9500 (tpp) cc_final: 0.9271 (tpt) REVERT: C 13 ASP cc_start: 0.8725 (p0) cc_final: 0.8431 (p0) REVERT: C 101 TRP cc_start: 0.8491 (p-90) cc_final: 0.7432 (p-90) REVERT: E 13 ASP cc_start: 0.8763 (p0) cc_final: 0.8447 (p0) REVERT: E 101 TRP cc_start: 0.8326 (p-90) cc_final: 0.7377 (p-90) REVERT: G 13 ASP cc_start: 0.8749 (p0) cc_final: 0.8366 (p0) REVERT: G 65 ILE cc_start: 0.9650 (mm) cc_final: 0.9412 (mm) REVERT: G 101 TRP cc_start: 0.8410 (p-90) cc_final: 0.7614 (p-90) REVERT: H 6 LEU cc_start: 0.9592 (mm) cc_final: 0.9392 (mm) REVERT: I 13 ASP cc_start: 0.8552 (p0) cc_final: 0.8229 (p0) REVERT: I 101 TRP cc_start: 0.8477 (p-90) cc_final: 0.7993 (p-90) REVERT: K 13 ASP cc_start: 0.8829 (p0) cc_final: 0.8470 (p0) REVERT: K 101 TRP cc_start: 0.8372 (p-90) cc_final: 0.7272 (p-90) REVERT: L 5 GLU cc_start: 0.9368 (mm-30) cc_final: 0.9111 (tp30) REVERT: M 13 ASP cc_start: 0.8762 (p0) cc_final: 0.8450 (p0) REVERT: M 101 TRP cc_start: 0.8431 (p-90) cc_final: 0.7440 (p-90) REVERT: N 5 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8859 (tp30) REVERT: N 6 LEU cc_start: 0.9541 (mm) cc_final: 0.9272 (mm) REVERT: O 13 ASP cc_start: 0.8664 (p0) cc_final: 0.8401 (p0) REVERT: P 5 GLU cc_start: 0.9331 (tp30) cc_final: 0.8982 (tp30) REVERT: Q 13 ASP cc_start: 0.8857 (p0) cc_final: 0.8497 (p0) REVERT: Q 101 TRP cc_start: 0.8400 (p-90) cc_final: 0.7708 (p-90) REVERT: R 6 LEU cc_start: 0.9698 (mm) cc_final: 0.9480 (mm) REVERT: S 9 MET cc_start: 0.9515 (tpp) cc_final: 0.9223 (tpp) REVERT: S 26 TYR cc_start: 0.9329 (t80) cc_final: 0.9088 (t80) REVERT: S 101 TRP cc_start: 0.8411 (p-90) cc_final: 0.7325 (p-90) REVERT: U 13 ASP cc_start: 0.8860 (p0) cc_final: 0.8526 (p0) REVERT: V 5 GLU cc_start: 0.9361 (mm-30) cc_final: 0.8998 (tp30) REVERT: V 30 LYS cc_start: 0.9369 (mmtt) cc_final: 0.8868 (tmtt) REVERT: W 13 ASP cc_start: 0.8815 (p0) cc_final: 0.8538 (p0) REVERT: W 101 TRP cc_start: 0.8397 (p-90) cc_final: 0.7806 (p-90) REVERT: X 3 LEU cc_start: 0.9097 (tt) cc_final: 0.8835 (tt) REVERT: X 30 LYS cc_start: 0.9260 (mmtt) cc_final: 0.8650 (tmtt) REVERT: Y 101 TRP cc_start: 0.8324 (p-90) cc_final: 0.7959 (p-90) REVERT: Z 5 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8939 (tp30) REVERT: Z 30 LYS cc_start: 0.9299 (mmtt) cc_final: 0.8829 (tmtt) REVERT: 0 101 TRP cc_start: 0.8492 (p-90) cc_final: 0.7809 (p-90) REVERT: 1 6 LEU cc_start: 0.9630 (mm) cc_final: 0.9416 (mm) REVERT: 1 30 LYS cc_start: 0.9392 (mmtt) cc_final: 0.8747 (tmtt) REVERT: 2 43 TYR cc_start: 0.8925 (p90) cc_final: 0.8667 (p90) REVERT: 2 101 TRP cc_start: 0.8401 (p-90) cc_final: 0.7431 (p-90) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.3005 time to fit residues: 105.3231 Evaluate side-chains 166 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 156 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 chunk 63 optimal weight: 0.2980 chunk 124 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 194 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.042845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.036131 restraints weight = 102329.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.037669 restraints weight = 54732.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.038748 restraints weight = 34256.262| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18585 Z= 0.129 Angle : 0.564 7.546 25335 Z= 0.298 Chirality : 0.044 0.194 3015 Planarity : 0.003 0.027 3225 Dihedral : 4.947 40.251 2565 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2385 helix: 2.40 (0.22), residues: 675 sheet: -1.18 (0.25), residues: 405 loop : -1.83 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP W 73 PHE 0.007 0.001 PHE D 51 TYR 0.013 0.001 TYR K 26 ARG 0.002 0.000 ARG P 41 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 660) hydrogen bonds : angle 4.24040 ( 1935) covalent geometry : bond 0.00275 (18585) covalent geometry : angle 0.56361 (25335) =============================================================================== Job complete usr+sys time: 5009.02 seconds wall clock time: 93 minutes 38.68 seconds (5618.68 seconds total)