Starting phenix.real_space_refine on Tue Jun 10 00:08:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u2b_41844/06_2025/8u2b_41844.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u2b_41844/06_2025/8u2b_41844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=0.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u2b_41844/06_2025/8u2b_41844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u2b_41844/06_2025/8u2b_41844.map" model { file = "/net/cci-nas-00/data/ceres_data/8u2b_41844/06_2025/8u2b_41844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u2b_41844/06_2025/8u2b_41844.cif" } resolution = 0.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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: 3 Type Number sf(0) Gaussians C 7400 2.51 5 N 1776 2.21 5 O 2220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11396 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "J" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "K" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "L" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "O" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "P" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "Q" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "R" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "S" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "T" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "U" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "V" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "W" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "X" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "Y" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "Z" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "a" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "b" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "c" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "d" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "e" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "f" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "g" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "h" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "i" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "j" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "k" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "l" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "m" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "n" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "o" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "p" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "q" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "r" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "s" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Time building chain proxies: 7.59, per 1000 atoms: 0.67 Number of scatterers: 11396 At special positions: 0 Unit cell: (59.34, 57.62, 249.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2220 8.00 N 1776 7.00 C 7400 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: 2.90 Conformation dependent library (CDL) restraints added in 1.6 seconds 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3034 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 0 sheets defined 95.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 27 through 57 removed outlier: 4.979A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 Processing helix chain 'J' and resid 27 through 57 removed outlier: 4.960A pdb=" N THR J 33 " --> pdb=" O VAL J 29 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 27 Processing helix chain 'K' and resid 27 through 58 removed outlier: 3.705A pdb=" N VAL K 32 " --> pdb=" O ALA K 28 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR K 33 " --> pdb=" O VAL K 29 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ALA K 34 " --> pdb=" O VAL K 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 27 Processing helix chain 'L' and resid 27 through 57 removed outlier: 3.673A pdb=" N VAL L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N THR L 33 " --> pdb=" O VAL L 29 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ALA L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 27 Processing helix chain 'M' and resid 27 through 57 removed outlier: 5.099A pdb=" N THR M 33 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA M 34 " --> pdb=" O VAL M 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 27 Processing helix chain 'N' and resid 27 through 57 removed outlier: 3.603A pdb=" N VAL N 32 " --> pdb=" O ALA N 28 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N THR N 33 " --> pdb=" O VAL N 29 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA N 34 " --> pdb=" O VAL N 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 27 Processing helix chain 'O' and resid 27 through 57 removed outlier: 3.632A pdb=" N VAL O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR O 33 " --> pdb=" O VAL O 29 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ALA O 34 " --> pdb=" O VAL O 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 27 Processing helix chain 'P' and resid 27 through 57 removed outlier: 3.540A pdb=" N VAL P 32 " --> pdb=" O ALA P 28 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR P 33 " --> pdb=" O VAL P 29 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA P 34 " --> pdb=" O VAL P 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 27 Processing helix chain 'Q' and resid 27 through 57 removed outlier: 3.576A pdb=" N VAL Q 32 " --> pdb=" O ALA Q 28 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N THR Q 33 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA Q 34 " --> pdb=" O VAL Q 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 27 Processing helix chain 'R' and resid 27 through 57 removed outlier: 3.599A pdb=" N VAL R 32 " --> pdb=" O ALA R 28 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR R 33 " --> pdb=" O VAL R 29 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 27 Processing helix chain 'S' and resid 27 through 57 removed outlier: 3.686A pdb=" N VAL S 32 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR S 33 " --> pdb=" O VAL S 29 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ALA S 34 " --> pdb=" O VAL S 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 27 Processing helix chain 'T' and resid 27 through 57 removed outlier: 3.522A pdb=" N VAL T 32 " --> pdb=" O ALA T 28 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR T 33 " --> pdb=" O VAL T 29 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ALA T 34 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 27 Processing helix chain 'U' and resid 27 through 57 removed outlier: 3.598A pdb=" N VAL U 32 " --> pdb=" O ALA U 28 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N THR U 33 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA U 34 " --> pdb=" O VAL U 30 " (cutoff:3.500A) Processing helix chain 'V' and resid 16 through 27 Processing helix chain 'V' and resid 27 through 57 removed outlier: 3.503A pdb=" N ILE V 31 " --> pdb=" O ILE V 27 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL V 32 " --> pdb=" O ALA V 28 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N THR V 33 " --> pdb=" O VAL V 29 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA V 34 " --> pdb=" O VAL V 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 16 through 27 Processing helix chain 'W' and resid 27 through 57 removed outlier: 3.612A pdb=" N VAL W 32 " --> pdb=" O ALA W 28 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N THR W 33 " --> pdb=" O VAL W 29 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA W 34 " --> pdb=" O VAL W 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 27 Processing helix chain 'X' and resid 27 through 57 removed outlier: 3.572A pdb=" N VAL X 32 " --> pdb=" O ALA X 28 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N THR X 33 " --> pdb=" O VAL X 29 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ALA X 34 " --> pdb=" O VAL X 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 27 through 57 removed outlier: 3.551A pdb=" N VAL Y 32 " --> pdb=" O ALA Y 28 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR Y 33 " --> pdb=" O VAL Y 29 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA Y 34 " --> pdb=" O VAL Y 30 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 27 through 57 removed outlier: 3.521A pdb=" N ILE Z 31 " --> pdb=" O ILE Z 27 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL Z 32 " --> pdb=" O ALA Z 28 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR Z 33 " --> pdb=" O VAL Z 29 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALA Z 34 " --> pdb=" O VAL Z 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 27 Processing helix chain 'a' and resid 27 through 57 removed outlier: 3.543A pdb=" N VAL a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THR a 33 " --> pdb=" O VAL a 29 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA a 34 " --> pdb=" O VAL a 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 27 Processing helix chain 'b' and resid 27 through 57 removed outlier: 3.663A pdb=" N VAL b 32 " --> pdb=" O ALA b 28 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N THR b 33 " --> pdb=" O VAL b 29 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA b 34 " --> pdb=" O VAL b 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 27 Processing helix chain 'c' and resid 27 through 57 removed outlier: 3.613A pdb=" N VAL c 32 " --> pdb=" O ALA c 28 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR c 33 " --> pdb=" O VAL c 29 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA c 34 " --> pdb=" O VAL c 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 27 Processing helix chain 'd' and resid 27 through 57 removed outlier: 3.630A pdb=" N VAL d 32 " --> pdb=" O ALA d 28 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N THR d 33 " --> pdb=" O VAL d 29 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA d 34 " --> pdb=" O VAL d 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 16 through 27 Processing helix chain 'e' and resid 27 through 57 removed outlier: 3.692A pdb=" N VAL e 32 " --> pdb=" O ALA e 28 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N THR e 33 " --> pdb=" O VAL e 29 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA e 34 " --> pdb=" O VAL e 30 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 27 Processing helix chain 'f' and resid 27 through 57 removed outlier: 3.641A pdb=" N VAL f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THR f 33 " --> pdb=" O VAL f 29 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ALA f 34 " --> pdb=" O VAL f 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 27 Processing helix chain 'g' and resid 27 through 57 removed outlier: 3.541A pdb=" N VAL g 32 " --> pdb=" O ALA g 28 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N THR g 33 " --> pdb=" O VAL g 29 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA g 34 " --> pdb=" O VAL g 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 16 through 27 Processing helix chain 'h' and resid 27 through 57 removed outlier: 3.597A pdb=" N VAL h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N THR h 33 " --> pdb=" O VAL h 29 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA h 34 " --> pdb=" O VAL h 30 " (cutoff:3.500A) Processing helix chain 'i' and resid 16 through 27 Processing helix chain 'i' and resid 27 through 57 removed outlier: 3.637A pdb=" N VAL i 32 " --> pdb=" O ALA i 28 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR i 33 " --> pdb=" O VAL i 29 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA i 34 " --> pdb=" O VAL i 30 " (cutoff:3.500A) Processing helix chain 'j' and resid 16 through 27 Processing helix chain 'j' and resid 27 through 57 removed outlier: 3.604A pdb=" N VAL j 32 " --> pdb=" O ALA j 28 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR j 33 " --> pdb=" O VAL j 29 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ALA j 34 " --> pdb=" O VAL j 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 27 Processing helix chain 'k' and resid 27 through 57 removed outlier: 3.604A pdb=" N VAL k 32 " --> pdb=" O ALA k 28 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N THR k 33 " --> pdb=" O VAL k 29 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA k 34 " --> pdb=" O VAL k 30 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 27 Processing helix chain 'l' and resid 27 through 57 removed outlier: 3.578A pdb=" N VAL l 32 " --> pdb=" O ALA l 28 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR l 33 " --> pdb=" O VAL l 29 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA l 34 " --> pdb=" O VAL l 30 " (cutoff:3.500A) Processing helix chain 'm' and resid 16 through 27 Processing helix chain 'm' and resid 27 through 57 removed outlier: 3.644A pdb=" N VAL m 32 " --> pdb=" O ALA m 28 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR m 33 " --> pdb=" O VAL m 29 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA m 34 " --> pdb=" O VAL m 30 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 27 Processing helix chain 'n' and resid 27 through 57 removed outlier: 3.587A pdb=" N VAL n 32 " --> pdb=" O ALA n 28 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N THR n 33 " --> pdb=" O VAL n 29 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA n 34 " --> pdb=" O VAL n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 27 Processing helix chain 'o' and resid 27 through 57 removed outlier: 3.589A pdb=" N VAL o 32 " --> pdb=" O ALA o 28 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N THR o 33 " --> pdb=" O VAL o 29 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ALA o 34 " --> pdb=" O VAL o 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 16 through 27 Processing helix chain 'p' and resid 27 through 57 removed outlier: 3.641A pdb=" N VAL p 32 " --> pdb=" O ALA p 28 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR p 33 " --> pdb=" O VAL p 29 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA p 34 " --> pdb=" O VAL p 30 " (cutoff:3.500A) Processing helix chain 'q' and resid 16 through 27 Processing helix chain 'q' and resid 27 through 57 removed outlier: 3.583A pdb=" N VAL q 32 " --> pdb=" O ALA q 28 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR q 33 " --> pdb=" O VAL q 29 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA q 34 " --> pdb=" O VAL q 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 16 through 27 Processing helix chain 'r' and resid 27 through 57 removed outlier: 5.119A pdb=" N THR r 33 " --> pdb=" O VAL r 29 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ALA r 34 " --> pdb=" O VAL r 30 " (cutoff:3.500A) Processing helix chain 's' and resid 16 through 27 Processing helix chain 's' and resid 27 through 57 removed outlier: 3.675A pdb=" N VAL s 32 " --> pdb=" O ALA s 28 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR s 33 " --> pdb=" O VAL s 29 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA s 34 " --> pdb=" O VAL s 30 " (cutoff:3.500A) 1188 hydrogen bonds defined for protein. 3564 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: 3.58 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 1813 1.28 - 1.35: 1665 1.35 - 1.42: 851 1.42 - 1.48: 1658 1.48 - 1.55: 5446 Bond restraints: 11433 Sorted by residual: bond pdb=" CB THR L 59 " pdb=" OG1 THR L 59 " ideal model delta sigma weight residual 1.433 1.397 0.036 1.60e-02 3.91e+03 5.03e+00 bond pdb=" CB THR J 59 " pdb=" OG1 THR J 59 " ideal model delta sigma weight residual 1.433 1.397 0.036 1.60e-02 3.91e+03 4.97e+00 bond pdb=" CB THR K 59 " pdb=" OG1 THR K 59 " ideal model delta sigma weight residual 1.433 1.399 0.034 1.60e-02 3.91e+03 4.56e+00 bond pdb=" CB THR i 36 " pdb=" OG1 THR i 36 " ideal model delta sigma weight residual 1.433 1.399 0.034 1.60e-02 3.91e+03 4.49e+00 bond pdb=" CB THR e 36 " pdb=" OG1 THR e 36 " ideal model delta sigma weight residual 1.433 1.399 0.034 1.60e-02 3.91e+03 4.47e+00 ... (remaining 11428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 9365 1.35 - 2.71: 3892 2.71 - 4.06: 1962 4.06 - 5.41: 456 5.41 - 6.76: 50 Bond angle restraints: 15725 Sorted by residual: angle pdb=" N VAL M 32 " pdb=" CA VAL M 32 " pdb=" C VAL M 32 " ideal model delta sigma weight residual 110.62 114.59 -3.97 1.02e+00 9.61e-01 1.52e+01 angle pdb=" CA ILE P 27 " pdb=" C ILE P 27 " pdb=" N ALA P 28 " ideal model delta sigma weight residual 117.37 120.24 -2.87 7.40e-01 1.83e+00 1.50e+01 angle pdb=" N THR W 16 " pdb=" CA THR W 16 " pdb=" C THR W 16 " ideal model delta sigma weight residual 111.33 115.92 -4.59 1.21e+00 6.83e-01 1.44e+01 angle pdb=" N THR q 16 " pdb=" CA THR q 16 " pdb=" C THR q 16 " ideal model delta sigma weight residual 111.33 115.89 -4.56 1.21e+00 6.83e-01 1.42e+01 angle pdb=" N THR m 16 " pdb=" CA THR m 16 " pdb=" C THR m 16 " ideal model delta sigma weight residual 111.33 115.70 -4.37 1.21e+00 6.83e-01 1.30e+01 ... (remaining 15720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 6498 16.07 - 32.14: 89 32.14 - 48.21: 1 48.21 - 64.29: 11 64.29 - 80.36: 24 Dihedral angle restraints: 6623 sinusoidal: 1924 harmonic: 4699 Sorted by residual: dihedral pdb=" C VAL U 29 " pdb=" N VAL U 29 " pdb=" CA VAL U 29 " pdb=" CB VAL U 29 " ideal model delta harmonic sigma weight residual -122.00 -130.27 8.27 0 2.50e+00 1.60e-01 1.09e+01 dihedral pdb=" N VAL U 29 " pdb=" C VAL U 29 " pdb=" CA VAL U 29 " pdb=" CB VAL U 29 " ideal model delta harmonic sigma weight residual 123.40 131.61 -8.21 0 2.50e+00 1.60e-01 1.08e+01 dihedral pdb=" C VAL f 29 " pdb=" N VAL f 29 " pdb=" CA VAL f 29 " pdb=" CB VAL f 29 " ideal model delta harmonic sigma weight residual -122.00 -130.19 8.19 0 2.50e+00 1.60e-01 1.07e+01 ... (remaining 6620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1107 0.048 - 0.096: 594 0.096 - 0.143: 587 0.143 - 0.191: 87 0.191 - 0.239: 30 Chirality restraints: 2405 Sorted by residual: chirality pdb=" CA VAL U 29 " pdb=" N VAL U 29 " pdb=" C VAL U 29 " pdb=" CB VAL U 29 " both_signs ideal model delta sigma weight residual False 2.44 2.20 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB THR A 16 " pdb=" CA THR A 16 " pdb=" OG1 THR A 16 " pdb=" CG2 THR A 16 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB THR M 16 " pdb=" CA THR M 16 " pdb=" OG1 THR M 16 " pdb=" CG2 THR M 16 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2402 not shown) Planarity restraints: 1813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR K 20 " -0.044 2.00e-02 2.50e+03 2.52e-02 1.27e+01 pdb=" CG TYR K 20 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR K 20 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR K 20 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR K 20 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR K 20 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR K 20 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR K 20 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 20 " -0.043 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR b 20 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR b 20 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR b 20 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR b 20 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR b 20 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR b 20 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR b 20 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 20 " -0.040 2.00e-02 2.50e+03 2.16e-02 9.32e+00 pdb=" CG TYR O 20 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR O 20 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR O 20 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR O 20 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR O 20 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR O 20 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR O 20 " -0.013 2.00e-02 2.50e+03 ... (remaining 1810 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.98: 5325 2.98 - 3.46: 13515 3.46 - 3.94: 19152 3.94 - 4.42: 20366 4.42 - 4.90: 35420 Nonbonded interactions: 93778 Sorted by model distance: nonbonded pdb=" OG SER J 54 " pdb=" OXT THR J 59 " model vdw 2.506 3.040 nonbonded pdb=" OG SER L 54 " pdb=" OXT THR L 59 " model vdw 2.516 3.040 nonbonded pdb=" OG SER Y 54 " pdb=" OXT THR Y 59 " model vdw 2.522 3.040 nonbonded pdb=" OG SER K 54 " pdb=" OXT THR K 59 " model vdw 2.522 3.040 nonbonded pdb=" OG SER g 54 " pdb=" OXT THR g 59 " model vdw 2.524 3.040 ... (remaining 93773 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.250 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 : 0.011 0.036 11433 Z= 0.690 Angle : 1.832 6.764 15725 Z= 1.194 Chirality : 0.081 0.239 2405 Planarity : 0.011 0.025 1813 Dihedral : 9.629 80.358 3589 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 0.09 (0.19), residues: 1591 helix: 0.20 (0.12), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.031 0.012 PHE s 46 TYR 0.044 0.011 TYR K 20 Details of bonding type rmsd hydrogen bonds : bond 0.17120 ( 1188) hydrogen bonds : angle 5.11900 ( 3564) covalent geometry : bond 0.01096 (11433) covalent geometry : angle 1.83244 (15725) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 1.152 Fit side-chains REVERT: N 19 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7265 (mt-10) REVERT: Q 19 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7174 (mt-10) REVERT: a 19 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7319 (mt-10) REVERT: n 19 GLU cc_start: 0.7586 (mt-10) cc_final: 0.6997 (mt-10) REVERT: q 41 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8273 (tttt) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.5459 time to fit residues: 266.2722 Evaluate side-chains 233 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.048000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.037221 restraints weight = 30726.555| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 2.04 r_work: 0.4145 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.4145 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11433 Z= 0.151 Angle : 0.534 5.843 15725 Z= 0.290 Chirality : 0.033 0.229 2405 Planarity : 0.002 0.009 1813 Dihedral : 8.851 84.311 1702 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.92 % Allowed : 16.74 % Favored : 81.34 % 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: 4.18 (0.21), residues: 1591 helix: 2.73 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE M 46 TYR 0.009 0.001 TYR A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04790 ( 1188) hydrogen bonds : angle 2.98281 ( 3564) covalent geometry : bond 0.00328 (11433) covalent geometry : angle 0.53437 (15725) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 242 time to evaluate : 1.864 Fit side-chains REVERT: o 19 GLU cc_start: 0.9466 (mt-10) cc_final: 0.9124 (mt-10) outliers start: 22 outliers final: 7 residues processed: 257 average time/residue: 0.6056 time to fit residues: 182.3257 Evaluate side-chains 204 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 29 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.047037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.035966 restraints weight = 31184.265| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.21 r_work: 0.4117 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3890 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11433 Z= 0.141 Angle : 0.502 6.686 15725 Z= 0.263 Chirality : 0.030 0.204 2405 Planarity : 0.002 0.010 1813 Dihedral : 8.218 89.941 1702 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.35 % Allowed : 20.58 % Favored : 77.07 % 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: 4.96 (0.21), residues: 1591 helix: 3.21 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE o 46 TYR 0.006 0.001 TYR A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 1188) hydrogen bonds : angle 2.95583 ( 3564) covalent geometry : bond 0.00324 (11433) covalent geometry : angle 0.50228 (15725) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 1.167 Fit side-chains REVERT: s 19 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8937 (mt-10) outliers start: 27 outliers final: 13 residues processed: 244 average time/residue: 0.5944 time to fit residues: 168.9448 Evaluate side-chains 209 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 29 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 10 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 0.0970 chunk 102 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.046652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.035673 restraints weight = 30736.552| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.03 r_work: 0.4143 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.4033 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9332 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11433 Z= 0.144 Angle : 0.492 6.289 15725 Z= 0.256 Chirality : 0.030 0.205 2405 Planarity : 0.002 0.011 1813 Dihedral : 7.850 89.902 1702 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.05 % Allowed : 21.19 % Favored : 75.76 % 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: 5.05 (0.21), residues: 1591 helix: 3.27 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE n 46 TYR 0.005 0.000 TYR o 20 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 1188) hydrogen bonds : angle 2.91603 ( 3564) covalent geometry : bond 0.00339 (11433) covalent geometry : angle 0.49217 (15725) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 1.245 Fit side-chains REVERT: n 19 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9172 (mt-10) REVERT: n 23 ILE cc_start: 0.9644 (mt) cc_final: 0.9430 (mp) REVERT: s 19 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8490 (mt-10) REVERT: s 41 LYS cc_start: 0.5482 (OUTLIER) cc_final: 0.3369 (mttt) outliers start: 35 outliers final: 16 residues processed: 242 average time/residue: 0.5646 time to fit residues: 159.7564 Evaluate side-chains 210 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 41 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 101 optimal weight: 0.0980 chunk 146 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.048231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.037126 restraints weight = 30647.654| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 2.26 r_work: 0.4173 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11433 Z= 0.114 Angle : 0.486 6.639 15725 Z= 0.251 Chirality : 0.029 0.183 2405 Planarity : 0.002 0.010 1813 Dihedral : 7.065 87.714 1702 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.96 % Allowed : 23.02 % Favored : 74.02 % 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: 4.98 (0.21), residues: 1591 helix: 3.22 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE n 46 TYR 0.007 0.001 TYR o 20 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 1188) hydrogen bonds : angle 2.86252 ( 3564) covalent geometry : bond 0.00236 (11433) covalent geometry : angle 0.48607 (15725) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 1.191 Fit side-chains REVERT: J 19 GLU cc_start: 0.5915 (OUTLIER) cc_final: 0.5508 (pt0) REVERT: m 19 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8724 (pt0) REVERT: o 19 GLU cc_start: 0.9395 (mt-10) cc_final: 0.9003 (OUTLIER) REVERT: q 19 GLU cc_start: 0.9497 (mt-10) cc_final: 0.8894 (OUTLIER) REVERT: r 19 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8866 (pt0) REVERT: s 19 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8944 (mt-10) REVERT: s 41 LYS cc_start: 0.4472 (OUTLIER) cc_final: 0.2875 (mttt) outliers start: 34 outliers final: 22 residues processed: 270 average time/residue: 0.5882 time to fit residues: 186.2391 Evaluate side-chains 226 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 41 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.047402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.036437 restraints weight = 30871.577| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.14 r_work: 0.4146 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9340 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11433 Z= 0.128 Angle : 0.503 8.935 15725 Z= 0.256 Chirality : 0.030 0.204 2405 Planarity : 0.002 0.022 1813 Dihedral : 6.568 87.835 1702 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.66 % Allowed : 23.28 % Favored : 73.06 % 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: 4.88 (0.21), residues: 1591 helix: 3.16 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE l 46 TYR 0.004 0.000 TYR o 20 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 1188) hydrogen bonds : angle 2.97026 ( 3564) covalent geometry : bond 0.00294 (11433) covalent geometry : angle 0.50292 (15725) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 1.235 Fit side-chains REVERT: K 23 ILE cc_start: 0.9445 (pp) cc_final: 0.9165 (mp) REVERT: m 19 GLU cc_start: 0.9427 (mt-10) cc_final: 0.8886 (OUTLIER) REVERT: o 19 GLU cc_start: 0.9427 (mt-10) cc_final: 0.8953 (OUTLIER) REVERT: q 31 ILE cc_start: 0.9173 (mm) cc_final: 0.8972 (mp) REVERT: s 19 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8761 (mt-10) REVERT: s 41 LYS cc_start: 0.5673 (OUTLIER) cc_final: 0.3616 (mttt) outliers start: 42 outliers final: 28 residues processed: 230 average time/residue: 0.4903 time to fit residues: 135.1813 Evaluate side-chains 214 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Y residue 22 LEU Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain i residue 22 LEU Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 41 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 0.0770 chunk 25 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.047849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.036650 restraints weight = 31553.740| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 2.09 r_work: 0.4184 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9330 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11433 Z= 0.116 Angle : 0.497 8.038 15725 Z= 0.252 Chirality : 0.030 0.187 2405 Planarity : 0.002 0.010 1813 Dihedral : 5.916 81.459 1702 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.92 % Allowed : 23.10 % Favored : 72.97 % 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: 4.83 (0.21), residues: 1591 helix: 3.13 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE k 46 TYR 0.005 0.000 TYR o 20 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 1188) hydrogen bonds : angle 2.91588 ( 3564) covalent geometry : bond 0.00251 (11433) covalent geometry : angle 0.49727 (15725) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 2.056 Fit side-chains REVERT: K 23 ILE cc_start: 0.9469 (pp) cc_final: 0.9181 (mp) REVERT: g 19 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8835 (pt0) REVERT: l 19 GLU cc_start: 0.9436 (mt-10) cc_final: 0.9036 (OUTLIER) REVERT: m 19 GLU cc_start: 0.9386 (mt-10) cc_final: 0.8846 (pt0) REVERT: o 19 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9011 (pt0) REVERT: q 19 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8549 (pt0) REVERT: r 19 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8556 (pt0) REVERT: s 19 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8638 (mt-10) REVERT: s 41 LYS cc_start: 0.5512 (OUTLIER) cc_final: 0.5310 (tttp) outliers start: 45 outliers final: 27 residues processed: 244 average time/residue: 0.6109 time to fit residues: 178.5965 Evaluate side-chains 224 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 41 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 0.0370 chunk 137 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 134 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.048134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.037165 restraints weight = 30786.685| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 2.02 r_work: 0.4191 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3965 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9320 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11433 Z= 0.117 Angle : 0.507 7.712 15725 Z= 0.258 Chirality : 0.030 0.212 2405 Planarity : 0.002 0.015 1813 Dihedral : 5.282 73.852 1702 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.49 % Allowed : 23.63 % Favored : 72.89 % 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: 4.79 (0.21), residues: 1591 helix: 3.10 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE n 46 TYR 0.006 0.001 TYR s 20 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 1188) hydrogen bonds : angle 2.96719 ( 3564) covalent geometry : bond 0.00256 (11433) covalent geometry : angle 0.50681 (15725) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 1.254 Fit side-chains REVERT: K 23 ILE cc_start: 0.9454 (pp) cc_final: 0.9166 (mp) REVERT: g 19 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8809 (pt0) REVERT: i 19 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8925 (pt0) REVERT: j 19 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8816 (pt0) REVERT: l 19 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9051 (OUTLIER) REVERT: m 19 GLU cc_start: 0.9396 (mt-10) cc_final: 0.8842 (pt0) REVERT: o 19 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9011 (pt0) REVERT: p 19 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8755 (pt0) REVERT: q 19 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8494 (pt0) REVERT: r 19 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8571 (pt0) REVERT: s 19 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8608 (mt-10) outliers start: 40 outliers final: 24 residues processed: 236 average time/residue: 0.4901 time to fit residues: 139.0831 Evaluate side-chains 223 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 29 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.047581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.036499 restraints weight = 30857.151| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 2.00 r_work: 0.4177 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.4057 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9323 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11433 Z= 0.125 Angle : 0.509 7.467 15725 Z= 0.259 Chirality : 0.030 0.230 2405 Planarity : 0.002 0.010 1813 Dihedral : 4.806 65.216 1702 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.14 % Allowed : 23.71 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.77 (0.21), residues: 1591 helix: 3.09 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE T 46 TYR 0.004 0.001 TYR p 20 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 1188) hydrogen bonds : angle 2.98724 ( 3564) covalent geometry : bond 0.00287 (11433) covalent geometry : angle 0.50903 (15725) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 1.930 Fit side-chains REVERT: K 23 ILE cc_start: 0.9454 (pp) cc_final: 0.9179 (mp) REVERT: g 19 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8766 (pt0) REVERT: i 19 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8905 (pt0) REVERT: j 19 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8793 (pt0) REVERT: l 19 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9026 (OUTLIER) REVERT: m 19 GLU cc_start: 0.9367 (mt-10) cc_final: 0.8796 (pt0) REVERT: n 19 GLU cc_start: 0.9386 (mt-10) cc_final: 0.8899 (pt0) REVERT: o 19 GLU cc_start: 0.9350 (mt-10) cc_final: 0.8879 (pt0) REVERT: p 19 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8743 (pt0) REVERT: q 19 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8394 (pt0) REVERT: r 19 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8522 (pt0) REVERT: s 19 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8714 (mt-10) outliers start: 36 outliers final: 27 residues processed: 231 average time/residue: 0.5997 time to fit residues: 166.3179 Evaluate side-chains 223 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 30 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain r residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 144 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.047175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.035722 restraints weight = 30410.901| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.17 r_work: 0.4106 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3968 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9344 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11433 Z= 0.144 Angle : 0.525 7.309 15725 Z= 0.269 Chirality : 0.031 0.207 2405 Planarity : 0.002 0.013 1813 Dihedral : 4.568 58.137 1702 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.70 % Allowed : 24.41 % Favored : 72.89 % 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: 4.73 (0.21), residues: 1591 helix: 3.07 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.000 PHE J 46 TYR 0.007 0.001 TYR o 20 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 1188) hydrogen bonds : angle 3.06081 ( 3564) covalent geometry : bond 0.00342 (11433) covalent geometry : angle 0.52471 (15725) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 1.257 Fit side-chains REVERT: K 23 ILE cc_start: 0.9464 (pp) cc_final: 0.9190 (mp) REVERT: l 19 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9022 (OUTLIER) REVERT: o 19 GLU cc_start: 0.9419 (mt-10) cc_final: 0.8932 (OUTLIER) REVERT: p 19 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8805 (pt0) REVERT: q 19 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8586 (pt0) REVERT: r 19 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8681 (pt0) REVERT: s 19 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8738 (mt-10) outliers start: 31 outliers final: 30 residues processed: 219 average time/residue: 0.5141 time to fit residues: 136.2559 Evaluate side-chains 216 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain d residue 22 LEU Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 30 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain m residue 31 ILE Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain r residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 143 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 0.0370 chunk 57 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.047169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.035917 restraints weight = 30183.783| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 1.98 r_work: 0.4126 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9330 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11433 Z= 0.136 Angle : 0.522 7.518 15725 Z= 0.266 Chirality : 0.031 0.310 2405 Planarity : 0.002 0.011 1813 Dihedral : 4.555 59.565 1702 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.05 % Allowed : 24.32 % Favored : 72.62 % 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: 4.72 (0.21), residues: 1591 helix: 3.06 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE T 46 TYR 0.004 0.001 TYR N 20 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 1188) hydrogen bonds : angle 3.03391 ( 3564) covalent geometry : bond 0.00316 (11433) covalent geometry : angle 0.52248 (15725) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 62653.18 seconds wall clock time: 1088 minutes 22.14 seconds (65302.14 seconds total)