Starting phenix.real_space_refine on Fri Jun 27 19:37:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f4x_28858/06_2025/8f4x_28858.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f4x_28858/06_2025/8f4x_28858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f4x_28858/06_2025/8f4x_28858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f4x_28858/06_2025/8f4x_28858.map" model { file = "/net/cci-nas-00/data/ceres_data/8f4x_28858/06_2025/8f4x_28858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f4x_28858/06_2025/8f4x_28858.cif" } resolution = 3.01 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= 0.003 sd= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 20580 2.51 5 N 6120 2.21 5 O 6000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 308 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32760 Number of models: 1 Model: "" Number of chains: 60 Chain: "0" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "1" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "2" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "3" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "4" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "5" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "6" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "7" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "8" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "9" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "A" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "B" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "C" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "D" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "F" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "G" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "H" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "I" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "J" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "K" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "L" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "M" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "N" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "O" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "P" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "Q" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "R" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "S" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "T" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "U" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "V" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "W" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "X" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "Y" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "Z" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "a" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "b" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "c" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "d" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "e" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "f" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "g" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "h" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "i" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "j" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "k" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "l" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "m" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "n" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "o" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "p" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "q" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "r" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "s" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "t" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "u" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "v" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "w" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Chain: "x" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 546 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 63} Time building chain proxies: 19.27, per 1000 atoms: 0.59 Number of scatterers: 32760 At special positions: 0 Unit cell: (153.12, 151.96, 151.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 6000 8.00 N 6120 7.00 C 20580 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: 8.41 Conformation dependent library (CDL) restraints added in 3.8 seconds 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 0 sheets defined 89.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain '0' and resid 1 through 20 Processing helix chain '0' and resid 22 through 37 Processing helix chain '0' and resid 39 through 50 removed outlier: 3.981A pdb=" N ALA 0 43 " --> pdb=" O PRO 0 39 " (cutoff:3.500A) Processing helix chain '0' and resid 53 through 65 Processing helix chain '1' and resid 2 through 20 Processing helix chain '1' and resid 22 through 37 Processing helix chain '1' and resid 39 through 50 removed outlier: 4.050A pdb=" N ALA 1 43 " --> pdb=" O PRO 1 39 " (cutoff:3.500A) Processing helix chain '1' and resid 53 through 65 Processing helix chain '2' and resid 2 through 20 Processing helix chain '2' and resid 22 through 37 Processing helix chain '2' and resid 39 through 51 removed outlier: 3.961A pdb=" N ALA 2 43 " --> pdb=" O PRO 2 39 " (cutoff:3.500A) Processing helix chain '2' and resid 53 through 65 Processing helix chain '3' and resid 2 through 21 removed outlier: 3.573A pdb=" N GLY 3 21 " --> pdb=" O LEU 3 17 " (cutoff:3.500A) Processing helix chain '3' and resid 22 through 36 removed outlier: 3.624A pdb=" N GLU 3 36 " --> pdb=" O ARG 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 39 through 50 removed outlier: 3.911A pdb=" N ALA 3 43 " --> pdb=" O PRO 3 39 " (cutoff:3.500A) Processing helix chain '3' and resid 53 through 65 Processing helix chain '4' and resid 2 through 21 removed outlier: 3.602A pdb=" N GLY 4 21 " --> pdb=" O LEU 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 22 through 36 removed outlier: 3.594A pdb=" N GLU 4 36 " --> pdb=" O ARG 4 32 " (cutoff:3.500A) Processing helix chain '4' and resid 39 through 50 removed outlier: 3.931A pdb=" N ALA 4 43 " --> pdb=" O PRO 4 39 " (cutoff:3.500A) Processing helix chain '4' and resid 53 through 65 Processing helix chain '5' and resid 2 through 20 removed outlier: 3.575A pdb=" N ALA 5 11 " --> pdb=" O ARG 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 37 Processing helix chain '5' and resid 39 through 50 removed outlier: 4.096A pdb=" N ALA 5 43 " --> pdb=" O PRO 5 39 " (cutoff:3.500A) Processing helix chain '5' and resid 53 through 65 Processing helix chain '6' and resid 2 through 20 Processing helix chain '6' and resid 22 through 36 Processing helix chain '6' and resid 39 through 50 removed outlier: 3.957A pdb=" N ALA 6 43 " --> pdb=" O PRO 6 39 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 65 Processing helix chain '7' and resid 2 through 20 Processing helix chain '7' and resid 22 through 36 Processing helix chain '7' and resid 39 through 52 removed outlier: 4.033A pdb=" N ALA 7 43 " --> pdb=" O PRO 7 39 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY 7 52 " --> pdb=" O LEU 7 48 " (cutoff:3.500A) Processing helix chain '7' and resid 53 through 65 Processing helix chain '8' and resid 2 through 20 Processing helix chain '8' and resid 22 through 37 Processing helix chain '8' and resid 39 through 50 removed outlier: 4.066A pdb=" N ALA 8 43 " --> pdb=" O PRO 8 39 " (cutoff:3.500A) Processing helix chain '8' and resid 53 through 65 Processing helix chain '9' and resid 2 through 20 Processing helix chain '9' and resid 22 through 37 removed outlier: 3.526A pdb=" N GLU 9 36 " --> pdb=" O ARG 9 32 " (cutoff:3.500A) Processing helix chain '9' and resid 39 through 50 removed outlier: 3.971A pdb=" N ALA 9 43 " --> pdb=" O PRO 9 39 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 65 Processing helix chain 'A' and resid 2 through 20 Processing helix chain 'A' and resid 22 through 36 removed outlier: 3.556A pdb=" N GLU A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 50 removed outlier: 3.995A pdb=" N ALA A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 50 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'B' and resid 2 through 20 Processing helix chain 'B' and resid 22 through 36 removed outlier: 3.669A pdb=" N GLU B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 50 removed outlier: 3.986A pdb=" N ALA B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'C' and resid 2 through 20 Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 39 through 50 removed outlier: 3.979A pdb=" N ALA C 43 " --> pdb=" O PRO C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 65 Processing helix chain 'D' and resid 2 through 20 Processing helix chain 'D' and resid 22 through 36 removed outlier: 3.506A pdb=" N GLU D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 50 removed outlier: 3.973A pdb=" N ALA D 43 " --> pdb=" O PRO D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 65 removed outlier: 3.579A pdb=" N ARG D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.556A pdb=" N GLY E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 36 removed outlier: 3.547A pdb=" N GLU E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 50 removed outlier: 4.008A pdb=" N ALA E 43 " --> pdb=" O PRO E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 65 Processing helix chain 'F' and resid 2 through 20 Processing helix chain 'F' and resid 22 through 37 Processing helix chain 'F' and resid 39 through 50 removed outlier: 4.016A pdb=" N ALA F 43 " --> pdb=" O PRO F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 65 Processing helix chain 'G' and resid 2 through 21 removed outlier: 3.628A pdb=" N GLY G 21 " --> pdb=" O LEU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 37 Processing helix chain 'G' and resid 39 through 52 removed outlier: 4.060A pdb=" N ALA G 43 " --> pdb=" O PRO G 39 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 65 Processing helix chain 'H' and resid 2 through 20 Processing helix chain 'H' and resid 22 through 36 Processing helix chain 'H' and resid 39 through 50 removed outlier: 4.033A pdb=" N ALA H 43 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 65 Processing helix chain 'I' and resid 2 through 20 Processing helix chain 'I' and resid 22 through 37 Processing helix chain 'I' and resid 39 through 51 removed outlier: 4.081A pdb=" N ALA I 43 " --> pdb=" O PRO I 39 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU I 50 " --> pdb=" O ARG I 46 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER I 51 " --> pdb=" O GLU I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 65 Processing helix chain 'J' and resid 2 through 20 Processing helix chain 'J' and resid 22 through 37 Processing helix chain 'J' and resid 39 through 50 removed outlier: 3.984A pdb=" N ALA J 43 " --> pdb=" O PRO J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 65 Processing helix chain 'K' and resid 2 through 20 Processing helix chain 'K' and resid 22 through 37 Processing helix chain 'K' and resid 39 through 50 removed outlier: 4.038A pdb=" N ALA K 43 " --> pdb=" O PRO K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 65 Processing helix chain 'L' and resid 2 through 20 Processing helix chain 'L' and resid 22 through 37 Processing helix chain 'L' and resid 39 through 50 removed outlier: 3.995A pdb=" N ALA L 43 " --> pdb=" O PRO L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 65 Processing helix chain 'M' and resid 2 through 20 Processing helix chain 'M' and resid 22 through 37 Processing helix chain 'M' and resid 39 through 52 removed outlier: 4.113A pdb=" N ALA M 43 " --> pdb=" O PRO M 39 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 65 Processing helix chain 'N' and resid 2 through 20 removed outlier: 3.514A pdb=" N ALA N 11 " --> pdb=" O ARG N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 37 Processing helix chain 'N' and resid 39 through 50 removed outlier: 4.014A pdb=" N ALA N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 65 Processing helix chain 'O' and resid 2 through 20 Processing helix chain 'O' and resid 22 through 36 Processing helix chain 'O' and resid 39 through 50 removed outlier: 3.987A pdb=" N ALA O 43 " --> pdb=" O PRO O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 65 Processing helix chain 'P' and resid 2 through 20 Processing helix chain 'P' and resid 22 through 36 Processing helix chain 'P' and resid 39 through 50 removed outlier: 4.061A pdb=" N ALA P 43 " --> pdb=" O PRO P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 65 Processing helix chain 'Q' and resid 2 through 20 Processing helix chain 'Q' and resid 22 through 36 Processing helix chain 'Q' and resid 39 through 50 removed outlier: 4.029A pdb=" N ALA Q 43 " --> pdb=" O PRO Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 65 Processing helix chain 'R' and resid 2 through 20 Processing helix chain 'R' and resid 22 through 36 Processing helix chain 'R' and resid 39 through 52 removed outlier: 3.997A pdb=" N ALA R 43 " --> pdb=" O PRO R 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU R 47 " --> pdb=" O ALA R 43 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 65 Processing helix chain 'S' and resid 2 through 20 Processing helix chain 'S' and resid 22 through 37 Processing helix chain 'S' and resid 39 through 50 removed outlier: 3.985A pdb=" N ALA S 43 " --> pdb=" O PRO S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 65 Processing helix chain 'T' and resid 2 through 20 Processing helix chain 'T' and resid 22 through 36 removed outlier: 3.786A pdb=" N GLU T 36 " --> pdb=" O ARG T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 removed outlier: 3.966A pdb=" N ALA T 43 " --> pdb=" O PRO T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 53 through 65 Processing helix chain 'U' and resid 2 through 20 Processing helix chain 'U' and resid 22 through 36 removed outlier: 3.607A pdb=" N GLU U 36 " --> pdb=" O ARG U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 39 through 50 removed outlier: 4.034A pdb=" N ALA U 43 " --> pdb=" O PRO U 39 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 65 Processing helix chain 'V' and resid 2 through 20 Processing helix chain 'V' and resid 22 through 37 Processing helix chain 'V' and resid 39 through 50 removed outlier: 3.892A pdb=" N ALA V 43 " --> pdb=" O PRO V 39 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 65 Processing helix chain 'W' and resid 2 through 20 Processing helix chain 'W' and resid 22 through 36 removed outlier: 3.594A pdb=" N GLU W 36 " --> pdb=" O ARG W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 50 removed outlier: 3.993A pdb=" N ALA W 43 " --> pdb=" O PRO W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 65 Processing helix chain 'X' and resid 2 through 20 Processing helix chain 'X' and resid 22 through 37 Processing helix chain 'X' and resid 39 through 52 removed outlier: 4.063A pdb=" N ALA X 43 " --> pdb=" O PRO X 39 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY X 52 " --> pdb=" O LEU X 48 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 65 Processing helix chain 'Y' and resid 2 through 20 Processing helix chain 'Y' and resid 22 through 37 Processing helix chain 'Y' and resid 39 through 52 removed outlier: 3.937A pdb=" N ALA Y 43 " --> pdb=" O PRO Y 39 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY Y 52 " --> pdb=" O LEU Y 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 53 through 65 Processing helix chain 'Z' and resid 2 through 20 Processing helix chain 'Z' and resid 22 through 36 removed outlier: 3.518A pdb=" N VAL Z 26 " --> pdb=" O ARG Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 39 through 50 removed outlier: 3.967A pdb=" N ALA Z 43 " --> pdb=" O PRO Z 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 53 through 65 Processing helix chain 'a' and resid 2 through 20 Processing helix chain 'a' and resid 22 through 36 removed outlier: 3.542A pdb=" N GLU a 36 " --> pdb=" O ARG a 32 " (cutoff:3.500A) Processing helix chain 'a' and resid 39 through 50 removed outlier: 3.982A pdb=" N ALA a 43 " --> pdb=" O PRO a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 65 Processing helix chain 'b' and resid 2 through 20 Processing helix chain 'b' and resid 22 through 36 removed outlier: 3.760A pdb=" N GLU b 36 " --> pdb=" O ARG b 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 39 through 50 removed outlier: 3.953A pdb=" N ALA b 43 " --> pdb=" O PRO b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 53 through 65 Processing helix chain 'c' and resid 2 through 20 Processing helix chain 'c' and resid 22 through 36 removed outlier: 3.579A pdb=" N GLU c 36 " --> pdb=" O ARG c 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 39 through 50 removed outlier: 3.890A pdb=" N ALA c 43 " --> pdb=" O PRO c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 53 through 65 Processing helix chain 'd' and resid 2 through 20 removed outlier: 3.650A pdb=" N ALA d 11 " --> pdb=" O ARG d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 22 through 36 removed outlier: 3.680A pdb=" N GLU d 36 " --> pdb=" O ARG d 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 39 through 50 removed outlier: 4.059A pdb=" N ALA d 43 " --> pdb=" O PRO d 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 65 Processing helix chain 'e' and resid 2 through 20 Processing helix chain 'e' and resid 22 through 36 removed outlier: 3.685A pdb=" N GLU e 36 " --> pdb=" O ARG e 32 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 52 removed outlier: 3.933A pdb=" N ALA e 43 " --> pdb=" O PRO e 39 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY e 52 " --> pdb=" O LEU e 48 " (cutoff:3.500A) Processing helix chain 'e' and resid 53 through 65 Processing helix chain 'f' and resid 2 through 20 Processing helix chain 'f' and resid 22 through 37 removed outlier: 3.503A pdb=" N GLU f 36 " --> pdb=" O ARG f 32 " (cutoff:3.500A) Processing helix chain 'f' and resid 39 through 50 removed outlier: 3.859A pdb=" N ALA f 43 " --> pdb=" O PRO f 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 53 through 65 Processing helix chain 'g' and resid 2 through 20 Processing helix chain 'g' and resid 22 through 36 removed outlier: 3.514A pdb=" N GLU g 36 " --> pdb=" O ARG g 32 " (cutoff:3.500A) Processing helix chain 'g' and resid 39 through 50 removed outlier: 3.977A pdb=" N ALA g 43 " --> pdb=" O PRO g 39 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 65 Processing helix chain 'h' and resid 2 through 20 removed outlier: 3.511A pdb=" N ALA h 11 " --> pdb=" O ARG h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 36 removed outlier: 3.524A pdb=" N GLU h 36 " --> pdb=" O ARG h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 39 through 50 removed outlier: 3.873A pdb=" N ALA h 43 " --> pdb=" O PRO h 39 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU h 47 " --> pdb=" O ALA h 43 " (cutoff:3.500A) Processing helix chain 'h' and resid 53 through 65 Processing helix chain 'i' and resid 2 through 20 Processing helix chain 'i' and resid 22 through 36 removed outlier: 3.617A pdb=" N GLU i 36 " --> pdb=" O ARG i 32 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 50 removed outlier: 4.009A pdb=" N ALA i 43 " --> pdb=" O PRO i 39 " (cutoff:3.500A) Processing helix chain 'i' and resid 53 through 65 Processing helix chain 'j' and resid 2 through 20 Processing helix chain 'j' and resid 22 through 36 Processing helix chain 'j' and resid 39 through 50 removed outlier: 3.936A pdb=" N ALA j 43 " --> pdb=" O PRO j 39 " (cutoff:3.500A) Processing helix chain 'j' and resid 53 through 65 Processing helix chain 'k' and resid 2 through 20 Processing helix chain 'k' and resid 22 through 36 Processing helix chain 'k' and resid 39 through 50 removed outlier: 3.941A pdb=" N ALA k 43 " --> pdb=" O PRO k 39 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 65 Processing helix chain 'l' and resid 2 through 20 Processing helix chain 'l' and resid 22 through 36 Processing helix chain 'l' and resid 39 through 50 removed outlier: 3.965A pdb=" N ALA l 43 " --> pdb=" O PRO l 39 " (cutoff:3.500A) Processing helix chain 'l' and resid 53 through 65 Processing helix chain 'm' and resid 2 through 20 Processing helix chain 'm' and resid 22 through 37 Processing helix chain 'm' and resid 39 through 52 removed outlier: 4.047A pdb=" N ALA m 43 " --> pdb=" O PRO m 39 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY m 52 " --> pdb=" O LEU m 48 " (cutoff:3.500A) Processing helix chain 'm' and resid 53 through 65 Processing helix chain 'n' and resid 2 through 20 Processing helix chain 'n' and resid 22 through 37 removed outlier: 3.525A pdb=" N GLU n 36 " --> pdb=" O ARG n 32 " (cutoff:3.500A) Processing helix chain 'n' and resid 39 through 50 removed outlier: 4.048A pdb=" N ALA n 43 " --> pdb=" O PRO n 39 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU n 50 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 53 through 65 Processing helix chain 'o' and resid 2 through 20 Processing helix chain 'o' and resid 22 through 36 removed outlier: 3.657A pdb=" N GLU o 36 " --> pdb=" O ARG o 32 " (cutoff:3.500A) Processing helix chain 'o' and resid 39 through 50 removed outlier: 3.961A pdb=" N ALA o 43 " --> pdb=" O PRO o 39 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 65 Processing helix chain 'p' and resid 2 through 21 removed outlier: 3.588A pdb=" N GLY p 21 " --> pdb=" O LEU p 17 " (cutoff:3.500A) Processing helix chain 'p' and resid 22 through 36 Processing helix chain 'p' and resid 39 through 50 removed outlier: 4.026A pdb=" N ALA p 43 " --> pdb=" O PRO p 39 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 65 Processing helix chain 'q' and resid 2 through 20 Processing helix chain 'q' and resid 22 through 36 removed outlier: 3.546A pdb=" N GLU q 36 " --> pdb=" O ARG q 32 " (cutoff:3.500A) Processing helix chain 'q' and resid 39 through 50 removed outlier: 4.010A pdb=" N ALA q 43 " --> pdb=" O PRO q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 53 through 65 Processing helix chain 'r' and resid 2 through 20 Processing helix chain 'r' and resid 22 through 36 removed outlier: 3.616A pdb=" N GLU r 36 " --> pdb=" O ARG r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 39 through 50 removed outlier: 4.016A pdb=" N ALA r 43 " --> pdb=" O PRO r 39 " (cutoff:3.500A) Processing helix chain 'r' and resid 53 through 65 Processing helix chain 's' and resid 2 through 21 removed outlier: 3.768A pdb=" N GLY s 21 " --> pdb=" O LEU s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 36 Processing helix chain 's' and resid 39 through 50 removed outlier: 4.056A pdb=" N ALA s 43 " --> pdb=" O PRO s 39 " (cutoff:3.500A) Processing helix chain 's' and resid 53 through 65 Processing helix chain 't' and resid 2 through 20 Processing helix chain 't' and resid 22 through 37 Processing helix chain 't' and resid 39 through 50 removed outlier: 4.061A pdb=" N ALA t 43 " --> pdb=" O PRO t 39 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 65 Processing helix chain 'u' and resid 2 through 21 removed outlier: 3.574A pdb=" N GLY u 21 " --> pdb=" O LEU u 17 " (cutoff:3.500A) Processing helix chain 'u' and resid 22 through 36 Processing helix chain 'u' and resid 39 through 50 removed outlier: 4.031A pdb=" N ALA u 43 " --> pdb=" O PRO u 39 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 65 Processing helix chain 'v' and resid 2 through 20 Processing helix chain 'v' and resid 22 through 36 Processing helix chain 'v' and resid 39 through 50 removed outlier: 4.048A pdb=" N ALA v 43 " --> pdb=" O PRO v 39 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 66 Processing helix chain 'w' and resid 2 through 20 Processing helix chain 'w' and resid 22 through 36 Processing helix chain 'w' and resid 39 through 50 removed outlier: 4.117A pdb=" N ALA w 43 " --> pdb=" O PRO w 39 " (cutoff:3.500A) Processing helix chain 'w' and resid 53 through 65 removed outlier: 3.622A pdb=" N ARG w 57 " --> pdb=" O ASP w 53 " (cutoff:3.500A) Processing helix chain 'x' and resid 2 through 20 Processing helix chain 'x' and resid 22 through 37 removed outlier: 3.551A pdb=" N GLU x 36 " --> pdb=" O ARG x 32 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 50 removed outlier: 4.048A pdb=" N ALA x 43 " --> pdb=" O PRO x 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 53 through 65 2518 hydrogen bonds defined for protein. 7554 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: 12.72 Time building geometry restraints manager: 9.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11940 1.34 - 1.46: 3858 1.46 - 1.57: 17202 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 33120 Sorted by residual: bond pdb=" C ASP G 53 " pdb=" O ASP G 53 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 8.03e-01 bond pdb=" C ASP b 53 " pdb=" O ASP b 53 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 7.24e-01 bond pdb=" CA ASP R 38 " pdb=" CB ASP R 38 " ideal model delta sigma weight residual 1.519 1.534 -0.014 1.73e-02 3.34e+03 6.99e-01 bond pdb=" C ASP t 53 " pdb=" O ASP t 53 " ideal model delta sigma weight residual 1.248 1.238 0.010 1.26e-02 6.30e+03 6.86e-01 bond pdb=" N ARG i 22 " pdb=" CA ARG i 22 " ideal model delta sigma weight residual 1.464 1.455 0.009 1.07e-02 8.73e+03 6.56e-01 ... (remaining 33115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 40127 0.86 - 1.71: 3653 1.71 - 2.57: 524 2.57 - 3.42: 192 3.42 - 4.28: 24 Bond angle restraints: 44520 Sorted by residual: angle pdb=" CA GLY R 52 " pdb=" C GLY R 52 " pdb=" N ASP R 53 " ideal model delta sigma weight residual 118.50 116.35 2.15 9.90e-01 1.02e+00 4.70e+00 angle pdb=" C LEU m 49 " pdb=" N GLU m 50 " pdb=" CA GLU m 50 " ideal model delta sigma weight residual 122.38 118.69 3.69 1.81e+00 3.05e-01 4.15e+00 angle pdb=" N GLY V 52 " pdb=" CA GLY V 52 " pdb=" C GLY V 52 " ideal model delta sigma weight residual 115.32 112.47 2.85 1.48e+00 4.57e-01 3.72e+00 angle pdb=" N GLY R 52 " pdb=" CA GLY R 52 " pdb=" C GLY R 52 " ideal model delta sigma weight residual 115.67 112.64 3.03 1.59e+00 3.96e-01 3.63e+00 angle pdb=" C LEU 2 49 " pdb=" N GLU 2 50 " pdb=" CA GLU 2 50 " ideal model delta sigma weight residual 122.38 118.98 3.40 1.81e+00 3.05e-01 3.52e+00 ... (remaining 44515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 18541 18.00 - 36.01: 1992 36.01 - 54.01: 285 54.01 - 72.01: 76 72.01 - 90.02: 106 Dihedral angle restraints: 21000 sinusoidal: 9360 harmonic: 11640 Sorted by residual: dihedral pdb=" CB GLU 3 47 " pdb=" CG GLU 3 47 " pdb=" CD GLU 3 47 " pdb=" OE1 GLU 3 47 " ideal model delta sinusoidal sigma weight residual 0.00 90.02 -90.02 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU F 36 " pdb=" CG GLU F 36 " pdb=" CD GLU F 36 " pdb=" OE1 GLU F 36 " ideal model delta sinusoidal sigma weight residual 0.00 89.91 -89.91 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " pdb=" CD GLU A 19 " pdb=" OE1 GLU A 19 " ideal model delta sinusoidal sigma weight residual 0.00 89.90 -89.90 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 20997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3132 0.026 - 0.052: 1416 0.052 - 0.078: 356 0.078 - 0.105: 77 0.105 - 0.131: 59 Chirality restraints: 5040 Sorted by residual: chirality pdb=" CA PRO w 54 " pdb=" N PRO w 54 " pdb=" C PRO w 54 " pdb=" CB PRO w 54 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA PRO D 54 " pdb=" N PRO D 54 " pdb=" C PRO D 54 " pdb=" CB PRO D 54 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA PRO v 23 " pdb=" N PRO v 23 " pdb=" C PRO v 23 " pdb=" CB PRO v 23 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 5037 not shown) Planarity restraints: 6000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP h 53 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.04e+00 pdb=" N PRO h 54 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO h 54 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO h 54 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 53 " -0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO K 54 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO K 54 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO K 54 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP 3 53 " -0.016 5.00e-02 4.00e+02 2.46e-02 9.70e-01 pdb=" N PRO 3 54 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO 3 54 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO 3 54 " -0.014 5.00e-02 4.00e+02 ... (remaining 5997 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5650 2.76 - 3.30: 32692 3.30 - 3.83: 53964 3.83 - 4.37: 59783 4.37 - 4.90: 104557 Nonbonded interactions: 256646 Sorted by model distance: nonbonded pdb=" NH1 ARG 6 22 " pdb=" OE2 GLU 6 25 " model vdw 2.226 3.120 nonbonded pdb=" N MET j 1 " pdb=" OE2 GLU j 4 " model vdw 2.275 3.120 nonbonded pdb=" N MET l 1 " pdb=" OE2 GLU l 4 " model vdw 2.286 3.120 nonbonded pdb=" OE1 GLU k 25 " pdb=" NH2 ARG k 28 " model vdw 2.295 3.120 nonbonded pdb=" O LEU 5 48 " pdb=" OG SER 5 51 " model vdw 2.302 3.040 ... (remaining 256641 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: 0.01 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' 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' 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' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } 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=0.00 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: 1.600 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: 0.030 Extract box with map and model: 1.210 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 69.990 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 33120 Z= 0.174 Angle : 0.549 4.276 44520 Z= 0.355 Chirality : 0.033 0.131 5040 Planarity : 0.003 0.026 6000 Dihedral : 15.823 90.016 13320 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % 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: 0.06 (0.12), residues: 3900 helix: 0.01 (0.08), residues: 3600 sheet: None (None), residues: 0 loop : 2.60 (0.24), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 8 PHE 0.015 0.002 PHE f 64 ARG 0.003 0.000 ARG p 46 Details of bonding type rmsd hydrogen bonds : bond 0.12748 ( 2518) hydrogen bonds : angle 5.54208 ( 7554) covalent geometry : bond 0.00382 (33120) covalent geometry : angle 0.54901 (44520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 4.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: k 7 ARG cc_start: 0.7714 (mtm180) cc_final: 0.7453 (mtp180) REVERT: v 7 ARG cc_start: 0.7809 (mtm180) cc_final: 0.7372 (ttm110) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.7000 time to fit residues: 158.7432 Evaluate side-chains 81 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.0470 chunk 272 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 282 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 8 HIS 1 8 HIS 2 8 HIS 3 8 HIS 4 8 HIS 5 8 HIS 6 8 HIS 7 8 HIS 8 8 HIS 9 8 HIS A 8 HIS B 8 HIS C 8 HIS D 8 HIS E 8 HIS F 8 HIS G 8 HIS H 8 HIS I 8 HIS J 8 HIS K 8 HIS L 8 HIS M 8 HIS N 8 HIS O 8 HIS P 8 HIS Q 8 HIS R 8 HIS S 8 HIS T 8 HIS U 8 HIS V 8 HIS W 8 HIS X 8 HIS Y 8 HIS Z 8 HIS a 8 HIS b 8 HIS c 8 HIS d 8 HIS e 8 HIS f 8 HIS g 8 HIS h 8 HIS i 8 HIS j 8 HIS k 8 HIS l 8 HIS m 8 HIS n 8 HIS o 8 HIS p 8 HIS q 8 HIS r 8 HIS s 8 HIS t 8 HIS u 8 HIS v 8 HIS w 8 HIS x 8 HIS Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.086267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.073955 restraints weight = 104888.578| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 3.59 r_work: 0.3423 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 33120 Z= 0.091 Angle : 0.431 5.601 44520 Z= 0.205 Chirality : 0.032 0.122 5040 Planarity : 0.004 0.031 6000 Dihedral : 3.626 28.311 4680 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Rotamer: Outliers : 0.45 % Allowed : 6.73 % Favored : 92.82 % 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: 3.11 (0.12), residues: 3900 helix: 1.99 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.97 (0.30), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 8 PHE 0.007 0.001 PHE G 42 ARG 0.008 0.000 ARG k 28 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 2518) hydrogen bonds : angle 3.11274 ( 7554) covalent geometry : bond 0.00204 (33120) covalent geometry : angle 0.43062 (44520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 4.039 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 113 average time/residue: 0.3859 time to fit residues: 78.1423 Evaluate side-chains 102 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 3.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 51 SER Chi-restraints excluded: chain 2 residue 64 PHE Chi-restraints excluded: chain 5 residue 51 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain O residue 64 PHE Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain U residue 64 PHE Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain u residue 64 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 245 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 353 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.085451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.073079 restraints weight = 105680.198| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 3.59 r_work: 0.3386 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33120 Z= 0.127 Angle : 0.419 4.137 44520 Z= 0.198 Chirality : 0.033 0.129 5040 Planarity : 0.004 0.034 6000 Dihedral : 3.412 24.157 4680 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 0.73 % Allowed : 8.82 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.00 (0.12), residues: 3900 helix: 2.58 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.81 (0.30), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 8 PHE 0.010 0.002 PHE L 64 ARG 0.006 0.000 ARG 4 57 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 2518) hydrogen bonds : angle 3.03661 ( 7554) covalent geometry : bond 0.00307 (33120) covalent geometry : angle 0.41876 (44520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 4.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 ASP cc_start: 0.8839 (t0) cc_final: 0.8627 (t0) REVERT: M 38 ASP cc_start: 0.8865 (t0) cc_final: 0.8656 (t70) REVERT: W 64 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.8243 (m-80) outliers start: 24 outliers final: 18 residues processed: 99 average time/residue: 0.3733 time to fit residues: 67.7842 Evaluate side-chains 95 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 4.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 64 PHE Chi-restraints excluded: chain 5 residue 51 SER Chi-restraints excluded: chain 8 residue 50 GLU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain O residue 64 PHE Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain T residue 50 GLU Chi-restraints excluded: chain U residue 64 PHE Chi-restraints excluded: chain V residue 64 PHE Chi-restraints excluded: chain W residue 64 PHE Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain u residue 64 PHE Chi-restraints excluded: chain x residue 64 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 37 optimal weight: 1.9990 chunk 288 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 305 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 302 optimal weight: 0.7980 chunk 291 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.085765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.074494 restraints weight = 106427.792| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.69 r_work: 0.3391 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 33120 Z= 0.102 Angle : 0.388 7.175 44520 Z= 0.184 Chirality : 0.032 0.125 5040 Planarity : 0.004 0.040 6000 Dihedral : 3.181 20.416 4680 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 1.09 % Allowed : 9.00 % Favored : 89.91 % 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: 4.54 (0.12), residues: 3900 helix: 2.93 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.76 (0.30), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 8 PHE 0.010 0.001 PHE L 64 ARG 0.004 0.000 ARG v 5 Details of bonding type rmsd hydrogen bonds : bond 0.02840 ( 2518) hydrogen bonds : angle 2.79503 ( 7554) covalent geometry : bond 0.00248 (33120) covalent geometry : angle 0.38812 (44520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 4.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 38 ASP cc_start: 0.8924 (t0) cc_final: 0.8719 (t70) REVERT: 3 48 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9154 (mp) REVERT: r 38 ASP cc_start: 0.8764 (t0) cc_final: 0.8557 (t0) outliers start: 36 outliers final: 28 residues processed: 118 average time/residue: 0.3783 time to fit residues: 81.0725 Evaluate side-chains 105 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 64 PHE Chi-restraints excluded: chain 3 residue 48 LEU Chi-restraints excluded: chain 5 residue 50 GLU Chi-restraints excluded: chain 5 residue 51 SER Chi-restraints excluded: chain 8 residue 50 GLU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 64 PHE Chi-restraints excluded: chain O residue 64 PHE Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain T residue 50 GLU Chi-restraints excluded: chain U residue 64 PHE Chi-restraints excluded: chain V residue 64 PHE Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain d residue 64 PHE Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain g residue 64 PHE Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain q residue 50 GLU Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain u residue 64 PHE Chi-restraints excluded: chain x residue 64 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 306 optimal weight: 0.8980 chunk 222 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 232 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 246 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.085665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.074464 restraints weight = 106367.050| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 3.67 r_work: 0.3395 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 33120 Z= 0.102 Angle : 0.389 6.759 44520 Z= 0.184 Chirality : 0.031 0.123 5040 Planarity : 0.004 0.037 6000 Dihedral : 3.045 17.801 4680 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 1.24 % Allowed : 9.82 % Favored : 88.94 % 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: 4.80 (0.12), residues: 3900 helix: 3.11 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.77 (0.30), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS p 8 PHE 0.010 0.001 PHE J 64 ARG 0.004 0.000 ARG v 5 Details of bonding type rmsd hydrogen bonds : bond 0.02786 ( 2518) hydrogen bonds : angle 2.73119 ( 7554) covalent geometry : bond 0.00245 (33120) covalent geometry : angle 0.38895 (44520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 81 time to evaluate : 3.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 48 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9136 (mp) REVERT: L 38 ASP cc_start: 0.8728 (t0) cc_final: 0.8483 (t0) REVERT: j 38 ASP cc_start: 0.8841 (t0) cc_final: 0.8597 (t0) REVERT: r 38 ASP cc_start: 0.8777 (t0) cc_final: 0.8571 (t0) outliers start: 41 outliers final: 33 residues processed: 118 average time/residue: 0.3698 time to fit residues: 79.1181 Evaluate side-chains 105 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 3.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 2 residue 64 PHE Chi-restraints excluded: chain 3 residue 48 LEU Chi-restraints excluded: chain 5 residue 50 GLU Chi-restraints excluded: chain 8 residue 50 GLU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 64 PHE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain O residue 64 PHE Chi-restraints excluded: chain P residue 50 GLU Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain T residue 50 GLU Chi-restraints excluded: chain U residue 64 PHE Chi-restraints excluded: chain V residue 64 PHE Chi-restraints excluded: chain W residue 64 PHE Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain q residue 29 LEU Chi-restraints excluded: chain q residue 50 GLU Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain u residue 64 PHE Chi-restraints excluded: chain x residue 64 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 251 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.085055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.072643 restraints weight = 105866.565| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.61 r_work: 0.3380 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 33120 Z= 0.135 Angle : 0.417 6.229 44520 Z= 0.198 Chirality : 0.033 0.123 5040 Planarity : 0.004 0.039 6000 Dihedral : 3.161 19.589 4680 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 1.42 % Allowed : 10.61 % Favored : 87.97 % 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: 4.72 (0.12), residues: 3900 helix: 3.07 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.45 (0.33), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 8 PHE 0.015 0.002 PHE L 64 ARG 0.003 0.000 ARG v 5 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 2518) hydrogen bonds : angle 2.86659 ( 7554) covalent geometry : bond 0.00328 (33120) covalent geometry : angle 0.41748 (44520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 68 time to evaluate : 4.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 48 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9137 (mp) REVERT: L 38 ASP cc_start: 0.8798 (t0) cc_final: 0.8556 (t0) REVERT: j 38 ASP cc_start: 0.8885 (t0) cc_final: 0.8626 (t0) REVERT: r 38 ASP cc_start: 0.8839 (t0) cc_final: 0.8630 (t0) outliers start: 47 outliers final: 36 residues processed: 109 average time/residue: 0.7167 time to fit residues: 137.5618 Evaluate side-chains 107 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 70 time to evaluate : 6.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 2 residue 51 SER Chi-restraints excluded: chain 2 residue 64 PHE Chi-restraints excluded: chain 3 residue 48 LEU Chi-restraints excluded: chain 8 residue 50 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain O residue 64 PHE Chi-restraints excluded: chain P residue 50 GLU Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain T residue 50 GLU Chi-restraints excluded: chain U residue 64 PHE Chi-restraints excluded: chain V residue 64 PHE Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 29 LEU Chi-restraints excluded: chain q residue 50 GLU Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain u residue 64 PHE Chi-restraints excluded: chain x residue 64 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 105 optimal weight: 6.9990 chunk 281 optimal weight: 2.9990 chunk 346 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 300 optimal weight: 2.9990 chunk 351 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.085150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.072832 restraints weight = 105969.525| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.58 r_work: 0.3383 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33120 Z= 0.122 Angle : 0.409 8.142 44520 Z= 0.193 Chirality : 0.032 0.123 5040 Planarity : 0.004 0.035 6000 Dihedral : 3.123 19.223 4680 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 1.52 % Allowed : 10.97 % Favored : 87.52 % 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: 4.81 (0.12), residues: 3900 helix: 3.13 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.46 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS p 8 PHE 0.012 0.002 PHE J 64 ARG 0.003 0.000 ARG v 5 Details of bonding type rmsd hydrogen bonds : bond 0.02909 ( 2518) hydrogen bonds : angle 2.79313 ( 7554) covalent geometry : bond 0.00298 (33120) covalent geometry : angle 0.40922 (44520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 70 time to evaluate : 3.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 48 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9135 (mp) REVERT: L 38 ASP cc_start: 0.8825 (t0) cc_final: 0.8604 (t0) REVERT: R 29 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8689 (tp) REVERT: j 38 ASP cc_start: 0.8919 (t0) cc_final: 0.8670 (t0) REVERT: r 38 ASP cc_start: 0.8842 (t0) cc_final: 0.8638 (t0) outliers start: 50 outliers final: 39 residues processed: 112 average time/residue: 0.3643 time to fit residues: 73.9479 Evaluate side-chains 111 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 70 time to evaluate : 3.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 29 LEU Chi-restraints excluded: chain 1 residue 29 LEU Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 2 residue 51 SER Chi-restraints excluded: chain 2 residue 64 PHE Chi-restraints excluded: chain 3 residue 48 LEU Chi-restraints excluded: chain 8 residue 50 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain O residue 64 PHE Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain T residue 50 GLU Chi-restraints excluded: chain U residue 64 PHE Chi-restraints excluded: chain V residue 64 PHE Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 29 LEU Chi-restraints excluded: chain q residue 50 GLU Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain u residue 64 PHE Chi-restraints excluded: chain x residue 64 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 121 optimal weight: 3.9990 chunk 321 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 246 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 265 optimal weight: 4.9990 chunk 349 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.084793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.072432 restraints weight = 105845.200| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.58 r_work: 0.3372 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 33120 Z= 0.141 Angle : 0.430 6.754 44520 Z= 0.202 Chirality : 0.033 0.122 5040 Planarity : 0.004 0.043 6000 Dihedral : 3.211 20.266 4680 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 1.52 % Allowed : 11.15 % Favored : 87.33 % 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 (0.12), residues: 3900 helix: 3.08 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.28 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS p 8 PHE 0.014 0.002 PHE q 64 ARG 0.003 0.000 ARG v 5 Details of bonding type rmsd hydrogen bonds : bond 0.03091 ( 2518) hydrogen bonds : angle 2.88041 ( 7554) covalent geometry : bond 0.00344 (33120) covalent geometry : angle 0.42963 (44520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 68 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 48 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9150 (mp) REVERT: L 38 ASP cc_start: 0.8875 (t0) cc_final: 0.8652 (t0) REVERT: R 29 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8721 (tp) REVERT: j 38 ASP cc_start: 0.8919 (t0) cc_final: 0.8678 (t0) REVERT: r 38 ASP cc_start: 0.8860 (t0) cc_final: 0.8615 (t0) outliers start: 50 outliers final: 41 residues processed: 112 average time/residue: 0.3668 time to fit residues: 74.2412 Evaluate side-chains 113 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 70 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 29 LEU Chi-restraints excluded: chain 1 residue 29 LEU Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 2 residue 51 SER Chi-restraints excluded: chain 2 residue 64 PHE Chi-restraints excluded: chain 3 residue 48 LEU Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 8 residue 50 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain O residue 64 PHE Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain T residue 50 GLU Chi-restraints excluded: chain U residue 64 PHE Chi-restraints excluded: chain V residue 64 PHE Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 29 LEU Chi-restraints excluded: chain q residue 50 GLU Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain u residue 64 PHE Chi-restraints excluded: chain x residue 64 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 344 optimal weight: 0.9980 chunk 315 optimal weight: 0.0040 chunk 215 optimal weight: 1.9990 chunk 359 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.085031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.072686 restraints weight = 106064.078| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.59 r_work: 0.3381 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33120 Z= 0.124 Angle : 0.416 6.567 44520 Z= 0.195 Chirality : 0.032 0.122 5040 Planarity : 0.004 0.039 6000 Dihedral : 3.150 19.594 4680 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 1.30 % Allowed : 11.61 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.84 (0.12), residues: 3900 helix: 3.15 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.39 (0.36), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS p 8 PHE 0.012 0.002 PHE J 64 ARG 0.004 0.000 ARG q 28 Details of bonding type rmsd hydrogen bonds : bond 0.02925 ( 2518) hydrogen bonds : angle 2.79539 ( 7554) covalent geometry : bond 0.00302 (33120) covalent geometry : angle 0.41601 (44520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 71 time to evaluate : 4.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 48 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9130 (mp) REVERT: L 38 ASP cc_start: 0.8871 (t0) cc_final: 0.8633 (t0) REVERT: R 29 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8700 (tp) REVERT: j 38 ASP cc_start: 0.8919 (t0) cc_final: 0.8676 (t0) REVERT: r 38 ASP cc_start: 0.8857 (t0) cc_final: 0.8628 (t0) outliers start: 43 outliers final: 40 residues processed: 108 average time/residue: 0.4234 time to fit residues: 83.6618 Evaluate side-chains 110 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 68 time to evaluate : 4.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 29 LEU Chi-restraints excluded: chain 1 residue 29 LEU Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 2 residue 51 SER Chi-restraints excluded: chain 2 residue 64 PHE Chi-restraints excluded: chain 3 residue 48 LEU Chi-restraints excluded: chain 8 residue 50 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain O residue 64 PHE Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain T residue 50 GLU Chi-restraints excluded: chain U residue 64 PHE Chi-restraints excluded: chain V residue 64 PHE Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 29 LEU Chi-restraints excluded: chain q residue 50 GLU Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain u residue 64 PHE Chi-restraints excluded: chain x residue 64 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 271 optimal weight: 6.9990 chunk 22 optimal weight: 0.0670 chunk 288 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 327 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 8 optimal weight: 0.0070 chunk 294 optimal weight: 0.9990 chunk 161 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.086601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.074413 restraints weight = 105603.031| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.62 r_work: 0.3424 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33120 Z= 0.078 Angle : 0.386 7.003 44520 Z= 0.181 Chirality : 0.030 0.118 5040 Planarity : 0.004 0.045 6000 Dihedral : 2.784 15.488 4680 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 1.00 % Allowed : 11.97 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 5.25 (0.12), residues: 3900 helix: 3.39 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 3.92 (0.34), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS i 8 PHE 0.006 0.001 PHE L 64 ARG 0.003 0.000 ARG q 28 Details of bonding type rmsd hydrogen bonds : bond 0.02390 ( 2518) hydrogen bonds : angle 2.49242 ( 7554) covalent geometry : bond 0.00180 (33120) covalent geometry : angle 0.38627 (44520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 3.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 38 ASP cc_start: 0.8890 (t0) cc_final: 0.8625 (t70) REVERT: L 38 ASP cc_start: 0.8840 (t0) cc_final: 0.8572 (t70) outliers start: 33 outliers final: 31 residues processed: 111 average time/residue: 0.3843 time to fit residues: 77.6540 Evaluate side-chains 108 residues out of total 3300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 4.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 2 residue 51 SER Chi-restraints excluded: chain 2 residue 64 PHE Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 8 residue 50 GLU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain E residue 64 PHE Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 50 GLU Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain O residue 64 PHE Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain R residue 64 PHE Chi-restraints excluded: chain T residue 50 GLU Chi-restraints excluded: chain U residue 64 PHE Chi-restraints excluded: chain V residue 64 PHE Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain f residue 50 GLU Chi-restraints excluded: chain i residue 50 GLU Chi-restraints excluded: chain o residue 50 GLU Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain p residue 51 SER Chi-restraints excluded: chain q residue 29 LEU Chi-restraints excluded: chain q residue 50 GLU Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain u residue 64 PHE Chi-restraints excluded: chain x residue 64 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 190 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 318 optimal weight: 5.9990 chunk 358 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 356 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.085923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.073705 restraints weight = 105729.642| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.60 r_work: 0.3410 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 33120 Z= 0.095 Angle : 0.406 7.086 44520 Z= 0.190 Chirality : 0.031 0.116 5040 Planarity : 0.004 0.041 6000 Dihedral : 2.792 16.678 4680 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 1.09 % Allowed : 12.03 % Favored : 86.88 % 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: 5.24 (0.12), residues: 3900 helix: 3.38 (0.08), residues: 3660 sheet: None (None), residues: 0 loop : 4.01 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS r 8 PHE 0.009 0.001 PHE L 64 ARG 0.003 0.000 ARG q 28 Details of bonding type rmsd hydrogen bonds : bond 0.02589 ( 2518) hydrogen bonds : angle 2.57647 ( 7554) covalent geometry : bond 0.00228 (33120) covalent geometry : angle 0.40557 (44520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11492.73 seconds wall clock time: 201 minutes 25.83 seconds (12085.83 seconds total)