Starting phenix.real_space_refine on Sat Jul 20 14:16:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u2b_41844/07_2024/8u2b_41844.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u2b_41844/07_2024/8u2b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u2b_41844/07_2024/8u2b_41844.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u2b_41844/07_2024/8u2b_41844.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u2b_41844/07_2024/8u2b_41844.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u2b_41844/07_2024/8u2b_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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 6.72, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.36 Conformation dependent library (CDL) restraints added in 1.9 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: 1.01 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: 3.50 Time building geometry restraints manager: 4.77 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: 104.04 - 108.54: 1065 108.54 - 113.04: 5557 113.04 - 117.54: 1659 117.54 - 122.04: 5866 122.04 - 126.54: 1578 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 2.440 nonbonded pdb=" OG SER L 54 " pdb=" OXT THR L 59 " model vdw 2.516 2.440 nonbonded pdb=" OG SER Y 54 " pdb=" OXT THR Y 59 " model vdw 2.522 2.440 nonbonded pdb=" OG SER K 54 " pdb=" OXT THR K 59 " model vdw 2.522 2.440 nonbonded pdb=" OG SER g 54 " pdb=" OXT THR g 59 " model vdw 2.524 2.440 ... (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 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: 2.850 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.860 Find NCS groups from input model: 0.580 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:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.700 ------------------------------------------------------------------------------- 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= 0.714 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 1.251 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: 0.5084 time to fit residues: 247.6523 Evaluate side-chains 233 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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: 1.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2710 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= 0.204 Angle : 0.528 5.891 15725 Z= 0.286 Chirality : 0.033 0.227 2405 Planarity : 0.002 0.009 1813 Dihedral : 9.412 75.954 1702 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.92 % Allowed : 16.48 % Favored : 81.60 % 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: 4.20 (0.21), residues: 1591 helix: 2.74 (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 O 46 TYR 0.008 0.001 TYR A 20 *********************** 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 261 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 239 time to evaluate : 1.113 Fit side-chains outliers start: 22 outliers final: 7 residues processed: 254 average time/residue: 0.5200 time to fit residues: 155.8857 Evaluate side-chains 201 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 194 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 74 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 11433 Z= 0.243 Angle : 0.514 8.178 15725 Z= 0.268 Chirality : 0.030 0.206 2405 Planarity : 0.002 0.010 1813 Dihedral : 8.748 71.160 1702 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.35 % Allowed : 20.49 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.95 (0.21), residues: 1591 helix: 3.20 (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 o 46 TYR 0.006 0.001 TYR r 20 *********************** 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 236 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 209 time to evaluate : 1.272 Fit side-chains outliers start: 27 outliers final: 13 residues processed: 227 average time/residue: 0.5511 time to fit residues: 147.0430 Evaluate side-chains 204 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 191 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 a residue 23 ILE 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 133 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11433 Z= 0.191 Angle : 0.495 9.106 15725 Z= 0.256 Chirality : 0.029 0.197 2405 Planarity : 0.002 0.011 1813 Dihedral : 8.618 71.215 1702 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.53 % Allowed : 20.75 % Favored : 76.72 % 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: 5.22 (0.21), residues: 1591 helix: 3.37 (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 0.004 0.000 TYR A 20 *********************** 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 243 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 214 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: s 41 LYS cc_start: 0.5367 (OUTLIER) cc_final: 0.3803 (mttt) outliers start: 29 outliers final: 15 residues processed: 232 average time/residue: 0.5245 time to fit residues: 144.2900 Evaluate side-chains 206 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 190 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain U residue 29 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 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 23 ILE 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 119 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11433 Z= 0.193 Angle : 0.497 6.543 15725 Z= 0.254 Chirality : 0.030 0.205 2405 Planarity : 0.002 0.022 1813 Dihedral : 8.329 71.104 1702 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.01 % Allowed : 21.19 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.16 (0.21), residues: 1591 helix: 3.33 (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 N 46 TYR 0.004 0.000 TYR q 20 *********************** 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 261 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 215 time to evaluate : 1.047 Fit side-chains REVERT: n 19 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7156 (mt-10) REVERT: s 41 LYS cc_start: 0.5304 (OUTLIER) cc_final: 0.3793 (mttt) outliers start: 46 outliers final: 24 residues processed: 244 average time/residue: 0.5166 time to fit residues: 148.8811 Evaluate side-chains 218 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 23 ILE Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain a residue 23 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain g residue 30 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 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 48 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11433 Z= 0.232 Angle : 0.508 6.215 15725 Z= 0.262 Chirality : 0.030 0.216 2405 Planarity : 0.002 0.023 1813 Dihedral : 8.343 73.052 1702 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.45 % Allowed : 21.27 % Favored : 74.28 % 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 0.002 0.000 PHE K 46 TYR 0.003 0.001 TYR K 20 *********************** 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 249 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 198 time to evaluate : 1.067 Fit side-chains REVERT: s 19 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7355 (mt-10) REVERT: s 41 LYS cc_start: 0.5329 (OUTLIER) cc_final: 0.3821 (mttt) outliers start: 51 outliers final: 30 residues processed: 224 average time/residue: 0.5039 time to fit residues: 134.2629 Evaluate side-chains 222 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 191 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 N residue 23 ILE Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain U residue 23 ILE 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 c residue 29 VAL 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 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 l residue 22 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q 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 138 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11433 Z= 0.177 Angle : 0.499 6.234 15725 Z= 0.256 Chirality : 0.030 0.192 2405 Planarity : 0.002 0.022 1813 Dihedral : 8.325 75.333 1702 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.01 % Allowed : 21.80 % Favored : 74.19 % 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 J 46 TYR 0.004 0.000 TYR m 20 *********************** 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 263 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 217 time to evaluate : 1.173 Fit side-chains REVERT: s 41 LYS cc_start: 0.5383 (OUTLIER) cc_final: 0.3904 (mttt) outliers start: 46 outliers final: 26 residues processed: 242 average time/residue: 0.4620 time to fit residues: 134.9140 Evaluate side-chains 227 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 a residue 22 LEU Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 42 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 h residue 29 VAL Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain l residue 22 LEU 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 41 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 0.0970 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11433 Z= 0.278 Angle : 0.532 6.494 15725 Z= 0.273 Chirality : 0.031 0.213 2405 Planarity : 0.002 0.019 1813 Dihedral : 8.342 77.103 1702 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.62 % Allowed : 21.62 % Favored : 73.76 % 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: 4.91 (0.21), residues: 1591 helix: 3.18 (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 0.004 0.001 TYR J 20 *********************** 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 247 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 194 time to evaluate : 1.258 Fit side-chains REVERT: s 41 LYS cc_start: 0.5359 (OUTLIER) cc_final: 0.3851 (mttt) outliers start: 53 outliers final: 35 residues processed: 229 average time/residue: 0.4952 time to fit residues: 135.2391 Evaluate side-chains 222 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 186 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 54 SER 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 S residue 31 ILE Chi-restraints excluded: chain U residue 23 ILE 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 22 LEU 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 e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain h residue 22 LEU Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain h residue 30 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 22 LEU Chi-restraints excluded: chain o residue 29 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11433 Z= 0.179 Angle : 0.519 6.793 15725 Z= 0.265 Chirality : 0.031 0.205 2405 Planarity : 0.002 0.023 1813 Dihedral : 8.496 80.313 1702 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.75 % Allowed : 22.49 % Favored : 73.76 % 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: 4.92 (0.21), residues: 1591 helix: 3.18 (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 0.005 0.000 TYR m 20 *********************** 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 250 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 207 time to evaluate : 1.226 Fit side-chains REVERT: s 41 LYS cc_start: 0.5324 (OUTLIER) cc_final: 0.3848 (mttt) outliers start: 43 outliers final: 25 residues processed: 232 average time/residue: 0.5082 time to fit residues: 140.4114 Evaluate side-chains 226 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL 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 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 29 VAL Chi-restraints excluded: chain f residue 22 LEU 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 i residue 22 LEU Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain o residue 22 LEU Chi-restraints excluded: chain o residue 29 VAL 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 41 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.0870 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 117 optimal weight: 0.0000 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.5566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11433 Z= 0.156 Angle : 0.509 7.706 15725 Z= 0.259 Chirality : 0.030 0.197 2405 Planarity : 0.002 0.021 1813 Dihedral : 7.983 79.593 1702 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.62 % Allowed : 23.80 % Favored : 73.58 % 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 (0.22), 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 0.002 0.000 PHE k 46 TYR 0.006 0.000 TYR s 20 ********************** 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 269 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 1.279 Fit side-chains outliers start: 30 outliers final: 20 residues processed: 258 average time/residue: 0.4585 time to fit residues: 143.4200 Evaluate side-chains 235 residues out of total 1147 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 215 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain K residue 29 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 X residue 30 VAL Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain a 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 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 l residue 22 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4558 r_free = 0.4558 target = 0.048006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.037039 restraints weight = 30596.084| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.06 r_work: 0.4104 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4031 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9301 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11433 Z= 0.176 Angle : 0.527 7.384 15725 Z= 0.267 Chirality : 0.031 0.214 2405 Planarity : 0.002 0.019 1813 Dihedral : 7.809 78.958 1702 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.62 % Allowed : 25.02 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.78 (0.22), 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 A 46 TYR 0.004 0.000 TYR s 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8323.28 seconds wall clock time: 147 minutes 1.45 seconds (8821.45 seconds total)