Starting phenix.real_space_refine on Fri Feb 16 21:37:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/02_2024/7n33_24137_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/02_2024/7n33_24137.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/02_2024/7n33_24137_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/02_2024/7n33_24137_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/02_2024/7n33_24137_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/02_2024/7n33_24137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/02_2024/7n33_24137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/02_2024/7n33_24137_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/02_2024/7n33_24137_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.039 sd= 0.161 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 66 5.16 5 C 10596 2.51 5 N 2676 2.21 5 O 3174 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16524 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2732 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 331} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Classifications: {'DNA': 2} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Classifications: {'DNA': 2} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Classifications: {'DNA': 2} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Classifications: {'DNA': 2} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Classifications: {'DNA': 2} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Classifications: {'DNA': 2} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 8.45, per 1000 atoms: 0.51 Number of scatterers: 16524 At special positions: 0 Unit cell: (107.555, 107.963, 123.095, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 6 15.00 F 6 9.00 O 3174 8.00 N 2676 7.00 C 10596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.07 Conformation dependent library (CDL) restraints added in 3.1 seconds 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 36 sheets defined 21.7% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 219 through 225 Processing helix chain 'A' and resid 233 through 236 No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 131 through 137 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 233 through 236 No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 300 through 309 Processing helix chain 'C' and resid 3 through 13 Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 131 through 137 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 219 through 225 Processing helix chain 'C' and resid 233 through 236 No H-bonds generated for 'chain 'C' and resid 233 through 236' Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 52 through 60 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 219 through 225 Processing helix chain 'D' and resid 233 through 236 No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 300 through 309 Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 52 through 60 Processing helix chain 'E' and resid 70 through 75 Processing helix chain 'E' and resid 115 through 117 No H-bonds generated for 'chain 'E' and resid 115 through 117' Processing helix chain 'E' and resid 131 through 137 Processing helix chain 'E' and resid 209 through 216 Processing helix chain 'E' and resid 219 through 225 Processing helix chain 'E' and resid 233 through 236 No H-bonds generated for 'chain 'E' and resid 233 through 236' Processing helix chain 'E' and resid 252 through 261 Processing helix chain 'E' and resid 300 through 309 Processing helix chain 'F' and resid 3 through 13 Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 70 through 75 Processing helix chain 'F' and resid 115 through 117 No H-bonds generated for 'chain 'F' and resid 115 through 117' Processing helix chain 'F' and resid 131 through 137 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 219 through 225 Processing helix chain 'F' and resid 233 through 236 No H-bonds generated for 'chain 'F' and resid 233 through 236' Processing helix chain 'F' and resid 252 through 261 Processing helix chain 'F' and resid 300 through 309 Processing sheet with id= A, first strand: chain 'A' and resid 25 through 28 removed outlier: 6.104A pdb=" N THR A 34 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLU A 42 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL A 36 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASP A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 122 through 125 removed outlier: 4.559A pdb=" N LYS A 181 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 160 through 163 Processing sheet with id= D, first strand: chain 'A' and resid 264 through 267 Processing sheet with id= E, first strand: chain 'A' and resid 276 through 279 Processing sheet with id= F, first strand: chain 'A' and resid 316 through 323 removed outlier: 5.647A pdb=" N LYS A 335 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL A 339 " --> pdb=" O LYS A 335 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 25 through 28 removed outlier: 6.103A pdb=" N THR B 34 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU B 42 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 36 " --> pdb=" O ASP B 40 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASP B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 122 through 125 removed outlier: 4.560A pdb=" N LYS B 181 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 160 through 163 Processing sheet with id= J, first strand: chain 'B' and resid 264 through 267 Processing sheet with id= K, first strand: chain 'B' and resid 276 through 279 Processing sheet with id= L, first strand: chain 'B' and resid 316 through 323 removed outlier: 5.647A pdb=" N LYS B 335 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 25 through 28 removed outlier: 6.105A pdb=" N THR C 34 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLU C 42 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL C 36 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASP C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 122 through 125 removed outlier: 4.559A pdb=" N LYS C 181 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 160 through 163 Processing sheet with id= P, first strand: chain 'C' and resid 264 through 267 Processing sheet with id= Q, first strand: chain 'C' and resid 276 through 279 Processing sheet with id= R, first strand: chain 'C' and resid 316 through 323 removed outlier: 5.647A pdb=" N LYS C 335 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL C 339 " --> pdb=" O LYS C 335 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 25 through 28 removed outlier: 6.104A pdb=" N THR D 34 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLU D 42 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL D 36 " --> pdb=" O ASP D 40 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASP D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 122 through 125 removed outlier: 4.561A pdb=" N LYS D 181 " --> pdb=" O GLN D 188 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 160 through 163 Processing sheet with id= V, first strand: chain 'D' and resid 264 through 267 Processing sheet with id= W, first strand: chain 'D' and resid 276 through 279 Processing sheet with id= X, first strand: chain 'D' and resid 316 through 323 removed outlier: 5.646A pdb=" N LYS D 335 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL D 339 " --> pdb=" O LYS D 335 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 25 through 28 removed outlier: 6.103A pdb=" N THR E 34 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLU E 42 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL E 36 " --> pdb=" O ASP E 40 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP E 40 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 122 through 125 removed outlier: 4.560A pdb=" N LYS E 181 " --> pdb=" O GLN E 188 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 160 through 163 Processing sheet with id= AB, first strand: chain 'E' and resid 264 through 267 Processing sheet with id= AC, first strand: chain 'E' and resid 276 through 279 Processing sheet with id= AD, first strand: chain 'E' and resid 316 through 323 removed outlier: 5.647A pdb=" N LYS E 335 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL E 339 " --> pdb=" O LYS E 335 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 25 through 28 removed outlier: 6.104A pdb=" N THR F 34 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLU F 42 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL F 36 " --> pdb=" O ASP F 40 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASP F 40 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 122 through 125 removed outlier: 4.559A pdb=" N LYS F 181 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 160 through 163 Processing sheet with id= AH, first strand: chain 'F' and resid 264 through 267 Processing sheet with id= AI, first strand: chain 'F' and resid 276 through 279 Processing sheet with id= AJ, first strand: chain 'F' and resid 316 through 323 removed outlier: 5.647A pdb=" N LYS F 335 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL F 339 " --> pdb=" O LYS F 335 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1260 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: 5.47 Time building geometry restraints manager: 6.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5239 1.33 - 1.45: 2266 1.45 - 1.57: 9253 1.57 - 1.69: 12 1.69 - 1.81: 102 Bond restraints: 16872 Sorted by residual: bond pdb=" C3' UFT G 401 " pdb=" C2' UFT G 401 " ideal model delta sigma weight residual 1.246 1.537 -0.291 2.00e-02 2.50e+03 2.12e+02 bond pdb=" C3' UFT K 401 " pdb=" C2' UFT K 401 " ideal model delta sigma weight residual 1.246 1.537 -0.291 2.00e-02 2.50e+03 2.11e+02 bond pdb=" C3' UFT I 401 " pdb=" C2' UFT I 401 " ideal model delta sigma weight residual 1.246 1.537 -0.291 2.00e-02 2.50e+03 2.11e+02 bond pdb=" C3' UFT H 401 " pdb=" C2' UFT H 401 " ideal model delta sigma weight residual 1.246 1.537 -0.291 2.00e-02 2.50e+03 2.11e+02 bond pdb=" C3' UFT L 401 " pdb=" C2' UFT L 401 " ideal model delta sigma weight residual 1.246 1.537 -0.291 2.00e-02 2.50e+03 2.11e+02 ... (remaining 16867 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.19: 553 107.19 - 113.90: 9682 113.90 - 120.61: 6456 120.61 - 127.32: 6058 127.32 - 134.04: 153 Bond angle restraints: 22902 Sorted by residual: angle pdb=" O3' UFT K 401 " pdb=" C3' UFT K 401 " pdb=" C2' UFT K 401 " ideal model delta sigma weight residual 110.03 119.22 -9.19 3.00e+00 1.11e-01 9.39e+00 angle pdb=" O3' UFT H 401 " pdb=" C3' UFT H 401 " pdb=" C2' UFT H 401 " ideal model delta sigma weight residual 110.03 119.22 -9.19 3.00e+00 1.11e-01 9.38e+00 angle pdb=" O3' UFT I 401 " pdb=" C3' UFT I 401 " pdb=" C2' UFT I 401 " ideal model delta sigma weight residual 110.03 119.21 -9.18 3.00e+00 1.11e-01 9.37e+00 angle pdb=" O3' UFT L 401 " pdb=" C3' UFT L 401 " pdb=" C2' UFT L 401 " ideal model delta sigma weight residual 110.03 119.19 -9.16 3.00e+00 1.11e-01 9.33e+00 angle pdb=" O3' UFT J 401 " pdb=" C3' UFT J 401 " pdb=" C2' UFT J 401 " ideal model delta sigma weight residual 110.03 119.18 -9.15 3.00e+00 1.11e-01 9.31e+00 ... (remaining 22897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.43: 9816 29.43 - 58.86: 210 58.86 - 88.29: 30 88.29 - 117.72: 6 117.72 - 147.15: 6 Dihedral angle restraints: 10068 sinusoidal: 4044 harmonic: 6024 Sorted by residual: dihedral pdb=" CA ILE C 28 " pdb=" C ILE C 28 " pdb=" N ASN C 29 " pdb=" CA ASN C 29 " ideal model delta harmonic sigma weight residual 180.00 -150.46 -29.54 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA ILE F 28 " pdb=" C ILE F 28 " pdb=" N ASN F 29 " pdb=" CA ASN F 29 " ideal model delta harmonic sigma weight residual -180.00 -150.47 -29.53 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA ILE E 28 " pdb=" C ILE E 28 " pdb=" N ASN E 29 " pdb=" CA ASN E 29 " ideal model delta harmonic sigma weight residual 180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 10065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2266 0.072 - 0.144: 350 0.144 - 0.215: 12 0.215 - 0.287: 0 0.287 - 0.359: 6 Chirality restraints: 2634 Sorted by residual: chirality pdb=" C2' UFT I 401 " pdb=" C3' UFT I 401 " pdb=" C1' UFT I 401 " pdb=" F2' UFT I 401 " both_signs ideal model delta sigma weight residual False 2.30 2.65 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C2' UFT J 401 " pdb=" C3' UFT J 401 " pdb=" C1' UFT J 401 " pdb=" F2' UFT J 401 " both_signs ideal model delta sigma weight residual False 2.30 2.65 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" C2' UFT G 401 " pdb=" C3' UFT G 401 " pdb=" C1' UFT G 401 " pdb=" F2' UFT G 401 " both_signs ideal model delta sigma weight residual False 2.30 2.65 -0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 2631 not shown) Planarity restraints: 2922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 296 " 0.004 2.00e-02 2.50e+03 8.46e-03 7.15e-01 pdb=" C ILE F 296 " -0.015 2.00e-02 2.50e+03 pdb=" O ILE F 296 " 0.006 2.00e-02 2.50e+03 pdb=" N ASP F 297 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 296 " -0.004 2.00e-02 2.50e+03 8.31e-03 6.91e-01 pdb=" C ILE A 296 " 0.014 2.00e-02 2.50e+03 pdb=" O ILE A 296 " -0.005 2.00e-02 2.50e+03 pdb=" N ASP A 297 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 296 " -0.004 2.00e-02 2.50e+03 8.30e-03 6.88e-01 pdb=" C ILE B 296 " 0.014 2.00e-02 2.50e+03 pdb=" O ILE B 296 " -0.005 2.00e-02 2.50e+03 pdb=" N ASP B 297 " -0.005 2.00e-02 2.50e+03 ... (remaining 2919 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 4915 2.82 - 3.34: 14711 3.34 - 3.86: 29634 3.86 - 4.38: 35382 4.38 - 4.90: 59015 Nonbonded interactions: 143657 Sorted by model distance: nonbonded pdb=" O LYS F 335 " pdb=" ND1 HIS F 338 " model vdw 2.294 2.520 nonbonded pdb=" O LYS A 335 " pdb=" ND1 HIS A 338 " model vdw 2.294 2.520 nonbonded pdb=" O LYS C 335 " pdb=" ND1 HIS C 338 " model vdw 2.294 2.520 nonbonded pdb=" O LYS B 335 " pdb=" ND1 HIS B 338 " model vdw 2.294 2.520 nonbonded pdb=" O LYS E 335 " pdb=" ND1 HIS E 338 " model vdw 2.295 2.520 ... (remaining 143652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 6.260 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 44.820 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.140 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:10.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.291 16872 Z= 0.696 Angle : 0.642 9.191 22902 Z= 0.318 Chirality : 0.051 0.359 2634 Planarity : 0.003 0.020 2922 Dihedral : 13.951 147.153 6180 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.93 % Allowed : 4.56 % Favored : 92.51 % 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: 0.50 (0.18), residues: 2064 helix: 0.66 (0.23), residues: 522 sheet: 1.00 (0.30), residues: 318 loop : 0.10 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 333 HIS 0.005 0.001 HIS D 96 PHE 0.014 0.002 PHE F 269 TYR 0.012 0.001 TYR F 33 ARG 0.003 0.000 ARG E 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 278 time to evaluate : 2.313 Fit side-chains REVERT: A 28 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8148 (mm) REVERT: A 201 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7709 (tp) REVERT: A 217 LEU cc_start: 0.7255 (mp) cc_final: 0.7024 (mp) REVERT: A 233 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7525 (t80) REVERT: A 255 LEU cc_start: 0.8299 (mp) cc_final: 0.7924 (mm) REVERT: A 343 TYR cc_start: 0.7035 (p90) cc_final: 0.5752 (p90) REVERT: B 28 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8151 (mm) REVERT: B 200 ASN cc_start: 0.8048 (t0) cc_final: 0.7842 (t0) REVERT: B 201 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7690 (tp) REVERT: B 217 LEU cc_start: 0.7253 (mp) cc_final: 0.6994 (mp) REVERT: B 233 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7260 (t80) REVERT: B 255 LEU cc_start: 0.8260 (mp) cc_final: 0.7891 (mm) REVERT: B 343 TYR cc_start: 0.7056 (p90) cc_final: 0.6234 (p90) REVERT: C 28 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8088 (mm) REVERT: C 201 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7726 (tp) REVERT: C 223 ILE cc_start: 0.7223 (mt) cc_final: 0.6928 (OUTLIER) REVERT: C 233 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7525 (t80) REVERT: C 255 LEU cc_start: 0.8277 (mp) cc_final: 0.7906 (mm) REVERT: C 343 TYR cc_start: 0.6997 (p90) cc_final: 0.6034 (p90) REVERT: D 28 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7937 (mm) REVERT: D 307 ILE cc_start: 0.8481 (tt) cc_final: 0.8090 (pt) REVERT: D 333 TRP cc_start: 0.7434 (m100) cc_final: 0.7056 (m100) REVERT: D 343 TYR cc_start: 0.8427 (p90) cc_final: 0.8114 (p90) REVERT: E 28 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7911 (mm) REVERT: E 233 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8031 (t80) REVERT: E 307 ILE cc_start: 0.8512 (tt) cc_final: 0.8118 (pt) REVERT: E 333 TRP cc_start: 0.7364 (m100) cc_final: 0.6949 (m100) REVERT: F 28 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7909 (mm) REVERT: F 307 ILE cc_start: 0.8536 (tt) cc_final: 0.8105 (pt) outliers start: 54 outliers final: 24 residues processed: 323 average time/residue: 1.3475 time to fit residues: 481.4185 Evaluate side-chains 215 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 179 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 233 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 119 optimal weight: 0.0470 chunk 185 optimal weight: 20.0000 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 235 HIS A 310 GLN B 310 GLN C 164 ASN C 310 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 HIS ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 338 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16872 Z= 0.179 Angle : 0.523 8.807 22902 Z= 0.269 Chirality : 0.049 0.408 2634 Planarity : 0.003 0.022 2922 Dihedral : 11.355 156.318 2319 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.75 % Allowed : 10.75 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2064 helix: 0.76 (0.23), residues: 534 sheet: 1.06 (0.29), residues: 318 loop : 0.16 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 333 HIS 0.012 0.001 HIS E 338 PHE 0.011 0.001 PHE C 269 TYR 0.013 0.001 TYR D 33 ARG 0.002 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 187 time to evaluate : 2.464 Fit side-chains revert: symmetry clash REVERT: A 233 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7493 (t80) REVERT: A 255 LEU cc_start: 0.8256 (mp) cc_final: 0.7881 (mm) REVERT: A 331 MET cc_start: 0.6501 (ttm) cc_final: 0.6198 (ttt) REVERT: B 200 ASN cc_start: 0.8021 (t0) cc_final: 0.7758 (t0) REVERT: B 233 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7252 (t80) REVERT: B 255 LEU cc_start: 0.8233 (mp) cc_final: 0.7879 (mm) REVERT: B 265 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7556 (mm-30) REVERT: B 343 TYR cc_start: 0.6870 (p90) cc_final: 0.6043 (p90) REVERT: C 233 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7508 (t80) REVERT: C 235 HIS cc_start: 0.6814 (t-170) cc_final: 0.6474 (t-90) REVERT: C 255 LEU cc_start: 0.8263 (mp) cc_final: 0.7911 (mm) REVERT: C 265 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6719 (mm-30) REVERT: C 343 TYR cc_start: 0.6850 (p90) cc_final: 0.6318 (p90) REVERT: D 205 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8287 (mtmm) REVERT: D 265 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6983 (tt0) REVERT: D 307 ILE cc_start: 0.8489 (tt) cc_final: 0.8072 (pt) REVERT: D 333 TRP cc_start: 0.7403 (m100) cc_final: 0.7139 (m100) REVERT: E 45 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: E 205 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8304 (mtmm) REVERT: E 233 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7877 (t80) REVERT: E 265 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6931 (tt0) REVERT: E 307 ILE cc_start: 0.8511 (tt) cc_final: 0.8118 (pt) REVERT: E 333 TRP cc_start: 0.7327 (m100) cc_final: 0.6857 (m100) REVERT: F 45 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: F 189 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7101 (mm110) REVERT: F 205 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8249 (mtmm) REVERT: F 307 ILE cc_start: 0.8506 (tt) cc_final: 0.8073 (pt) REVERT: F 341 THR cc_start: 0.7661 (m) cc_final: 0.7336 (m) outliers start: 69 outliers final: 26 residues processed: 234 average time/residue: 1.3056 time to fit residues: 340.3097 Evaluate side-chains 204 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 165 optimal weight: 30.0000 chunk 184 optimal weight: 3.9990 chunk 63 optimal weight: 40.0000 chunk 148 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16872 Z= 0.228 Angle : 0.528 8.362 22902 Z= 0.273 Chirality : 0.049 0.378 2634 Planarity : 0.003 0.023 2922 Dihedral : 11.137 163.796 2289 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.02 % Allowed : 12.32 % Favored : 83.66 % 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: 0.54 (0.18), residues: 2064 helix: 0.71 (0.23), residues: 534 sheet: 1.00 (0.29), residues: 318 loop : 0.11 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 333 HIS 0.010 0.001 HIS D 338 PHE 0.012 0.001 PHE D 269 TYR 0.012 0.001 TYR E 33 ARG 0.002 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 173 time to evaluate : 1.998 Fit side-chains REVERT: A 233 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7356 (t80) REVERT: A 343 TYR cc_start: 0.6973 (p90) cc_final: 0.6471 (p90) REVERT: B 200 ASN cc_start: 0.8228 (t0) cc_final: 0.7934 (t0) REVERT: B 201 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7543 (tm) REVERT: B 233 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7315 (t80) REVERT: B 343 TYR cc_start: 0.6876 (p90) cc_final: 0.6538 (p90) REVERT: C 201 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7637 (tm) REVERT: C 233 PHE cc_start: 0.7784 (OUTLIER) cc_final: 0.7416 (t80) REVERT: C 235 HIS cc_start: 0.6758 (t-170) cc_final: 0.6418 (t-90) REVERT: C 265 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6784 (mm-30) REVERT: C 343 TYR cc_start: 0.6859 (p90) cc_final: 0.6564 (p90) REVERT: D 189 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7024 (mm-40) REVERT: D 205 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8293 (mtmm) REVERT: D 307 ILE cc_start: 0.8481 (tt) cc_final: 0.8051 (pt) REVERT: D 333 TRP cc_start: 0.7403 (m100) cc_final: 0.7140 (m100) REVERT: E 45 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: E 189 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7045 (mm-40) REVERT: E 205 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8335 (mtmm) REVERT: E 233 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7862 (t80) REVERT: E 307 ILE cc_start: 0.8492 (tt) cc_final: 0.8080 (pt) REVERT: E 333 TRP cc_start: 0.7356 (m100) cc_final: 0.7011 (m100) REVERT: F 45 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: F 189 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7184 (mm110) REVERT: F 205 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8231 (mtmm) REVERT: F 307 ILE cc_start: 0.8496 (tt) cc_final: 0.8072 (pt) REVERT: F 341 THR cc_start: 0.7646 (m) cc_final: 0.7307 (m) outliers start: 74 outliers final: 29 residues processed: 226 average time/residue: 1.2488 time to fit residues: 315.6739 Evaluate side-chains 212 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 168 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 318 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 96 optimal weight: 30.0000 chunk 20 optimal weight: 20.0000 chunk 88 optimal weight: 0.1980 chunk 124 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 chunk 197 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 176 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 overall best weight: 6.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16872 Z= 0.252 Angle : 0.537 8.289 22902 Z= 0.279 Chirality : 0.049 0.385 2634 Planarity : 0.003 0.023 2922 Dihedral : 11.007 166.029 2287 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.34 % Allowed : 12.43 % Favored : 83.22 % 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: 0.48 (0.18), residues: 2064 helix: 0.64 (0.23), residues: 534 sheet: 1.01 (0.29), residues: 318 loop : 0.07 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 333 HIS 0.010 0.001 HIS D 338 PHE 0.013 0.001 PHE D 269 TYR 0.012 0.001 TYR E 33 ARG 0.002 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 177 time to evaluate : 2.165 Fit side-chains REVERT: A 28 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.8014 (mm) REVERT: A 219 MET cc_start: 0.7240 (ttm) cc_final: 0.6785 (ttp) REVERT: A 233 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7261 (t80) REVERT: A 265 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7118 (mm-30) REVERT: A 343 TYR cc_start: 0.6903 (p90) cc_final: 0.6609 (p90) REVERT: B 200 ASN cc_start: 0.8214 (t0) cc_final: 0.7912 (t0) REVERT: B 201 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7686 (tm) REVERT: B 212 ILE cc_start: 0.8057 (mt) cc_final: 0.7852 (mp) REVERT: B 343 TYR cc_start: 0.7052 (p90) cc_final: 0.6613 (p90) REVERT: C 233 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7321 (t80) REVERT: C 235 HIS cc_start: 0.6746 (t-170) cc_final: 0.6398 (t-90) REVERT: C 265 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6778 (mm-30) REVERT: C 343 TYR cc_start: 0.7040 (p90) cc_final: 0.6653 (p90) REVERT: D 28 ILE cc_start: 0.7982 (OUTLIER) cc_final: 0.7777 (mm) REVERT: D 189 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7050 (mm-40) REVERT: D 205 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8296 (mtmm) REVERT: D 265 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: D 307 ILE cc_start: 0.8487 (tt) cc_final: 0.8057 (pt) REVERT: D 333 TRP cc_start: 0.7413 (m100) cc_final: 0.7176 (m100) REVERT: E 45 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: E 189 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7077 (mm-40) REVERT: E 205 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8304 (mtmm) REVERT: E 307 ILE cc_start: 0.8486 (tt) cc_final: 0.8063 (pt) REVERT: F 45 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: F 189 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7202 (mm110) REVERT: F 205 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8229 (mtmm) REVERT: F 307 ILE cc_start: 0.8507 (tt) cc_final: 0.8081 (pt) REVERT: F 341 THR cc_start: 0.7627 (m) cc_final: 0.7293 (m) outliers start: 80 outliers final: 37 residues processed: 232 average time/residue: 1.2022 time to fit residues: 312.7163 Evaluate side-chains 224 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 171 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 97 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 322 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 chunk 176 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16872 Z= 0.204 Angle : 0.514 8.230 22902 Z= 0.267 Chirality : 0.049 0.383 2634 Planarity : 0.003 0.024 2922 Dihedral : 10.576 166.509 2275 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.13 % Allowed : 13.30 % Favored : 82.57 % 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: 0.52 (0.18), residues: 2064 helix: 0.71 (0.23), residues: 534 sheet: 1.02 (0.29), residues: 318 loop : 0.08 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 333 HIS 0.010 0.001 HIS D 338 PHE 0.011 0.001 PHE D 269 TYR 0.012 0.001 TYR F 33 ARG 0.002 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 174 time to evaluate : 2.156 Fit side-chains REVERT: A 28 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7922 (mm) REVERT: A 219 MET cc_start: 0.7221 (ttm) cc_final: 0.6767 (ttp) REVERT: A 265 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7128 (mm-30) REVERT: A 343 TYR cc_start: 0.7044 (p90) cc_final: 0.6686 (p90) REVERT: B 28 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7878 (mm) REVERT: B 200 ASN cc_start: 0.8188 (t0) cc_final: 0.7899 (t0) REVERT: B 201 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7740 (tm) REVERT: B 212 ILE cc_start: 0.8062 (mt) cc_final: 0.7853 (mp) REVERT: B 343 TYR cc_start: 0.7012 (p90) cc_final: 0.6683 (p90) REVERT: C 28 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7886 (mm) REVERT: C 233 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7228 (t80) REVERT: C 235 HIS cc_start: 0.6766 (t-170) cc_final: 0.6413 (t-90) REVERT: C 343 TYR cc_start: 0.7011 (p90) cc_final: 0.6654 (p90) REVERT: D 189 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7035 (mm-40) REVERT: D 205 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8280 (mtmm) REVERT: D 265 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6992 (tt0) REVERT: D 307 ILE cc_start: 0.8479 (tt) cc_final: 0.8051 (pt) REVERT: D 333 TRP cc_start: 0.7389 (m100) cc_final: 0.7168 (m100) REVERT: E 45 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: E 189 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7076 (mm-40) REVERT: E 205 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8335 (mtmm) REVERT: E 233 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7903 (t80) REVERT: E 265 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: E 307 ILE cc_start: 0.8470 (tt) cc_final: 0.8064 (pt) REVERT: F 45 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: F 189 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7198 (mm110) REVERT: F 205 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8226 (mtmm) REVERT: F 265 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6875 (tt0) REVERT: F 307 ILE cc_start: 0.8504 (tt) cc_final: 0.8081 (pt) REVERT: F 341 THR cc_start: 0.7616 (m) cc_final: 0.7280 (m) outliers start: 76 outliers final: 28 residues processed: 227 average time/residue: 1.1886 time to fit residues: 303.1366 Evaluate side-chains 216 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 170 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 341 THR Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 265 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 20.0000 chunk 177 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 48 optimal weight: 40.0000 chunk 197 optimal weight: 0.6980 chunk 163 optimal weight: 8.9990 chunk 91 optimal weight: 0.6980 chunk 16 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 overall best weight: 2.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 164 ASN C 164 ASN D 29 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS E 29 ASN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16872 Z= 0.133 Angle : 0.491 8.260 22902 Z= 0.254 Chirality : 0.048 0.378 2634 Planarity : 0.003 0.024 2922 Dihedral : 10.342 166.698 2273 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.58 % Allowed : 14.17 % Favored : 82.25 % 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: 0.70 (0.18), residues: 2064 helix: 0.88 (0.23), residues: 534 sheet: 1.12 (0.29), residues: 318 loop : 0.19 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 333 HIS 0.005 0.001 HIS D 338 PHE 0.008 0.001 PHE D 269 TYR 0.011 0.001 TYR E 33 ARG 0.001 0.000 ARG C 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 189 time to evaluate : 2.044 Fit side-chains REVERT: A 223 ILE cc_start: 0.7234 (mt) cc_final: 0.7024 (pt) REVERT: A 265 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7279 (mm-30) REVERT: A 343 TYR cc_start: 0.6947 (p90) cc_final: 0.6632 (p90) REVERT: B 200 ASN cc_start: 0.8156 (t0) cc_final: 0.7857 (t0) REVERT: B 212 ILE cc_start: 0.8066 (mt) cc_final: 0.7858 (mp) REVERT: B 235 HIS cc_start: 0.6727 (t-170) cc_final: 0.6515 (t-90) REVERT: B 343 TYR cc_start: 0.6948 (p90) cc_final: 0.6633 (p90) REVERT: C 200 ASN cc_start: 0.7938 (t0) cc_final: 0.7721 (t0) REVERT: C 223 ILE cc_start: 0.7238 (mt) cc_final: 0.7020 (pt) REVERT: C 233 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7329 (t80) REVERT: C 235 HIS cc_start: 0.6759 (t-170) cc_final: 0.6434 (t-90) REVERT: C 343 TYR cc_start: 0.6945 (p90) cc_final: 0.6587 (p90) REVERT: D 189 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7037 (mm-40) REVERT: D 205 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8300 (mtmm) REVERT: D 233 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7715 (t80) REVERT: D 265 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6945 (tt0) REVERT: D 307 ILE cc_start: 0.8463 (tt) cc_final: 0.8088 (pt) REVERT: D 333 TRP cc_start: 0.7390 (m100) cc_final: 0.7179 (m100) REVERT: E 45 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: E 47 LYS cc_start: 0.8951 (mmtm) cc_final: 0.8188 (mmtp) REVERT: E 189 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7071 (mm-40) REVERT: E 205 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8318 (mtmm) REVERT: E 233 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7846 (t80) REVERT: E 265 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7123 (tt0) REVERT: E 307 ILE cc_start: 0.8453 (tt) cc_final: 0.8059 (pt) REVERT: F 45 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: F 189 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7164 (mm110) REVERT: F 205 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8232 (mtmm) REVERT: F 265 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6835 (tt0) REVERT: F 307 ILE cc_start: 0.8479 (tt) cc_final: 0.8075 (pt) REVERT: F 341 THR cc_start: 0.7589 (m) cc_final: 0.7257 (m) outliers start: 66 outliers final: 30 residues processed: 237 average time/residue: 1.2298 time to fit residues: 329.0957 Evaluate side-chains 216 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 172 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 265 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16872 Z= 0.143 Angle : 0.502 8.219 22902 Z= 0.258 Chirality : 0.048 0.378 2634 Planarity : 0.003 0.025 2922 Dihedral : 10.335 166.761 2273 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.42 % Allowed : 14.98 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2064 helix: 0.93 (0.23), residues: 534 sheet: 1.48 (0.30), residues: 282 loop : 0.27 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 333 HIS 0.007 0.001 HIS D 338 PHE 0.009 0.001 PHE F 269 TYR 0.012 0.001 TYR E 33 ARG 0.002 0.000 ARG C 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 179 time to evaluate : 2.273 Fit side-chains REVERT: A 223 ILE cc_start: 0.7212 (mt) cc_final: 0.7011 (pt) REVERT: A 255 LEU cc_start: 0.8206 (mp) cc_final: 0.7696 (tp) REVERT: A 265 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7269 (mm-30) REVERT: A 343 TYR cc_start: 0.6920 (p90) cc_final: 0.6571 (p90) REVERT: B 200 ASN cc_start: 0.8167 (t0) cc_final: 0.7891 (t0) REVERT: B 212 ILE cc_start: 0.8069 (mt) cc_final: 0.7865 (mp) REVERT: B 235 HIS cc_start: 0.6718 (t-170) cc_final: 0.6505 (t-90) REVERT: B 343 TYR cc_start: 0.6941 (p90) cc_final: 0.6627 (p90) REVERT: C 200 ASN cc_start: 0.7961 (t0) cc_final: 0.7728 (t0) REVERT: C 223 ILE cc_start: 0.7236 (mt) cc_final: 0.7015 (pt) REVERT: C 233 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.7381 (t80) REVERT: C 235 HIS cc_start: 0.6763 (t-170) cc_final: 0.6442 (t-90) REVERT: C 343 TYR cc_start: 0.6937 (p90) cc_final: 0.6574 (p90) REVERT: D 189 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7020 (mm-40) REVERT: D 205 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8292 (mtmm) REVERT: D 233 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7737 (t80) REVERT: D 265 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6943 (tt0) REVERT: D 307 ILE cc_start: 0.8492 (tt) cc_final: 0.8100 (pt) REVERT: D 333 TRP cc_start: 0.7406 (m100) cc_final: 0.7174 (m100) REVERT: E 45 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: E 47 LYS cc_start: 0.8954 (mmtm) cc_final: 0.8208 (mmtp) REVERT: E 189 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7085 (mm-40) REVERT: E 205 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8316 (mtmm) REVERT: E 265 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: E 307 ILE cc_start: 0.8452 (tt) cc_final: 0.8062 (pt) REVERT: F 45 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: F 189 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7159 (mm110) REVERT: F 205 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8231 (mtmm) REVERT: F 265 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6853 (tt0) REVERT: F 307 ILE cc_start: 0.8497 (tt) cc_final: 0.8072 (pt) REVERT: F 341 THR cc_start: 0.7590 (m) cc_final: 0.7264 (m) outliers start: 63 outliers final: 34 residues processed: 226 average time/residue: 1.1892 time to fit residues: 301.2877 Evaluate side-chains 218 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 170 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 265 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 133 optimal weight: 0.2980 chunk 97 optimal weight: 40.0000 chunk 18 optimal weight: 9.9990 chunk 154 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 overall best weight: 5.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16872 Z= 0.225 Angle : 0.549 10.730 22902 Z= 0.281 Chirality : 0.050 0.383 2634 Planarity : 0.003 0.028 2922 Dihedral : 10.508 166.645 2273 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.58 % Allowed : 14.88 % Favored : 81.54 % 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: 0.68 (0.18), residues: 2064 helix: 0.79 (0.23), residues: 534 sheet: 1.42 (0.30), residues: 282 loop : 0.15 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 333 HIS 0.008 0.001 HIS D 338 PHE 0.012 0.001 PHE D 269 TYR 0.013 0.001 TYR D 33 ARG 0.002 0.000 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 176 time to evaluate : 2.619 Fit side-chains REVERT: A 255 LEU cc_start: 0.8215 (mp) cc_final: 0.7723 (tp) REVERT: A 265 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7116 (mm-30) REVERT: A 343 TYR cc_start: 0.6997 (p90) cc_final: 0.6631 (p90) REVERT: B 200 ASN cc_start: 0.8209 (t0) cc_final: 0.7896 (t0) REVERT: B 343 TYR cc_start: 0.6979 (p90) cc_final: 0.6609 (p90) REVERT: C 200 ASN cc_start: 0.8016 (t0) cc_final: 0.7785 (t0) REVERT: C 233 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7342 (t80) REVERT: C 235 HIS cc_start: 0.6778 (t-170) cc_final: 0.6441 (t-90) REVERT: C 331 MET cc_start: 0.6628 (ttt) cc_final: 0.6330 (ttt) REVERT: C 343 TYR cc_start: 0.7023 (p90) cc_final: 0.6450 (p90) REVERT: D 189 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7054 (mm-40) REVERT: D 205 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8267 (mtmm) REVERT: D 265 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6991 (tt0) REVERT: D 307 ILE cc_start: 0.8500 (tt) cc_final: 0.8080 (pt) REVERT: D 333 TRP cc_start: 0.7379 (m100) cc_final: 0.7101 (m100) REVERT: E 45 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: E 189 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7101 (mm-40) REVERT: E 205 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8328 (mtmm) REVERT: E 233 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7883 (t80) REVERT: E 265 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7145 (tt0) REVERT: E 307 ILE cc_start: 0.8474 (tt) cc_final: 0.8073 (pt) REVERT: F 45 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: F 189 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7228 (mm110) REVERT: F 205 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8231 (mtmm) REVERT: F 265 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6888 (tt0) REVERT: F 307 ILE cc_start: 0.8515 (tt) cc_final: 0.8093 (pt) REVERT: F 341 THR cc_start: 0.7589 (m) cc_final: 0.7257 (m) outliers start: 66 outliers final: 36 residues processed: 227 average time/residue: 1.2093 time to fit residues: 308.8178 Evaluate side-chains 218 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 168 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 265 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 6.9990 chunk 171 optimal weight: 0.4980 chunk 183 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 182 optimal weight: 0.8980 chunk 120 optimal weight: 20.0000 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16872 Z= 0.185 Angle : 0.541 12.825 22902 Z= 0.274 Chirality : 0.049 0.381 2634 Planarity : 0.003 0.028 2922 Dihedral : 10.452 166.573 2273 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.64 % Allowed : 15.15 % Favored : 81.22 % 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: 0.60 (0.18), residues: 2064 helix: 0.77 (0.23), residues: 534 sheet: 1.06 (0.29), residues: 318 loop : 0.13 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 333 HIS 0.009 0.001 HIS D 338 PHE 0.011 0.001 PHE D 269 TYR 0.012 0.001 TYR F 33 ARG 0.001 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 169 time to evaluate : 2.126 Fit side-chains REVERT: A 255 LEU cc_start: 0.8209 (mp) cc_final: 0.7710 (tp) REVERT: A 265 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: A 343 TYR cc_start: 0.6970 (p90) cc_final: 0.6734 (p90) REVERT: B 200 ASN cc_start: 0.8185 (t0) cc_final: 0.7880 (t0) REVERT: B 343 TYR cc_start: 0.6935 (p90) cc_final: 0.6728 (p90) REVERT: C 200 ASN cc_start: 0.8020 (t0) cc_final: 0.7781 (t0) REVERT: C 233 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7316 (t80) REVERT: C 235 HIS cc_start: 0.6775 (t-170) cc_final: 0.6439 (t-90) REVERT: C 343 TYR cc_start: 0.6991 (p90) cc_final: 0.6639 (p90) REVERT: D 189 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7046 (mm-40) REVERT: D 205 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8282 (mtmm) REVERT: D 265 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6974 (tt0) REVERT: D 307 ILE cc_start: 0.8493 (tt) cc_final: 0.8081 (pt) REVERT: D 333 TRP cc_start: 0.7375 (m100) cc_final: 0.7171 (m100) REVERT: D 341 THR cc_start: 0.7587 (m) cc_final: 0.7265 (m) REVERT: E 45 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: E 189 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7105 (mm-40) REVERT: E 205 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8321 (mtmm) REVERT: E 233 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7878 (t80) REVERT: E 265 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7135 (tt0) REVERT: E 307 ILE cc_start: 0.8467 (tt) cc_final: 0.8068 (pt) REVERT: E 343 TYR cc_start: 0.8302 (p90) cc_final: 0.7992 (p90) REVERT: F 45 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: F 189 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7190 (mm110) REVERT: F 205 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8235 (mtmm) REVERT: F 265 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6873 (tt0) REVERT: F 307 ILE cc_start: 0.8516 (tt) cc_final: 0.8093 (pt) REVERT: F 341 THR cc_start: 0.7590 (m) cc_final: 0.7261 (m) outliers start: 67 outliers final: 41 residues processed: 219 average time/residue: 1.2278 time to fit residues: 303.8536 Evaluate side-chains 222 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 167 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 301 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 91 optimal weight: 50.0000 chunk 134 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 187 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 125 optimal weight: 0.8980 chunk 99 optimal weight: 30.0000 chunk 128 optimal weight: 6.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16872 Z= 0.259 Angle : 0.584 13.583 22902 Z= 0.296 Chirality : 0.050 0.385 2634 Planarity : 0.003 0.029 2922 Dihedral : 10.596 166.425 2273 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.64 % Allowed : 15.20 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2064 helix: 0.60 (0.23), residues: 534 sheet: 1.18 (0.31), residues: 282 loop : 0.16 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 333 HIS 0.009 0.001 HIS D 338 PHE 0.014 0.002 PHE D 269 TYR 0.012 0.001 TYR F 33 ARG 0.002 0.000 ARG C 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 166 time to evaluate : 1.950 Fit side-chains REVERT: A 265 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7118 (mm-30) REVERT: A 343 TYR cc_start: 0.7154 (p90) cc_final: 0.6809 (p90) REVERT: B 200 ASN cc_start: 0.8203 (t0) cc_final: 0.7911 (t0) REVERT: B 343 TYR cc_start: 0.7101 (p90) cc_final: 0.6714 (p90) REVERT: C 200 ASN cc_start: 0.8043 (t0) cc_final: 0.7814 (t0) REVERT: C 233 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7290 (t80) REVERT: C 235 HIS cc_start: 0.6768 (t-170) cc_final: 0.6416 (t-90) REVERT: C 343 TYR cc_start: 0.7030 (p90) cc_final: 0.6747 (p90) REVERT: D 189 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7070 (mm-40) REVERT: D 205 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8272 (mtmm) REVERT: D 265 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6997 (tt0) REVERT: D 307 ILE cc_start: 0.8502 (tt) cc_final: 0.8080 (pt) REVERT: D 333 TRP cc_start: 0.7425 (m100) cc_final: 0.7154 (m100) REVERT: D 341 THR cc_start: 0.7580 (m) cc_final: 0.7263 (m) REVERT: E 45 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: E 189 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7121 (mm-40) REVERT: E 205 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8301 (mtmm) REVERT: E 233 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7908 (t80) REVERT: E 265 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7132 (tt0) REVERT: E 307 ILE cc_start: 0.8478 (tt) cc_final: 0.8064 (pt) REVERT: E 343 TYR cc_start: 0.8325 (p90) cc_final: 0.8059 (p90) REVERT: F 45 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: F 189 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7210 (mm110) REVERT: F 205 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8226 (mtmm) REVERT: F 265 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: F 307 ILE cc_start: 0.8524 (tt) cc_final: 0.8102 (pt) REVERT: F 341 THR cc_start: 0.7593 (m) cc_final: 0.7261 (m) outliers start: 67 outliers final: 42 residues processed: 216 average time/residue: 1.1664 time to fit residues: 283.4825 Evaluate side-chains 220 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 164 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 338 HIS Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 338 HIS Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 338 HIS Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 189 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 203 GLU Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 29 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 45 GLU Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 189 GLN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 205 LYS Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 189 GLN Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 322 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 162 optimal weight: 0.0870 chunk 67 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 40.0000 chunk 142 optimal weight: 2.9990 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.140702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.100343 restraints weight = 21601.509| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.78 r_work: 0.3200 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16872 Z= 0.159 Angle : 0.546 13.663 22902 Z= 0.275 Chirality : 0.049 0.378 2634 Planarity : 0.003 0.034 2922 Dihedral : 10.445 166.304 2273 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.26 % Allowed : 15.64 % Favored : 81.11 % 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: 0.68 (0.18), residues: 2064 helix: 0.71 (0.23), residues: 534 sheet: 1.40 (0.30), residues: 282 loop : 0.20 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 333 HIS 0.008 0.001 HIS D 338 PHE 0.009 0.001 PHE B 259 TYR 0.011 0.001 TYR E 33 ARG 0.001 0.000 ARG A 258 =============================================================================== Job complete usr+sys time: 7053.14 seconds wall clock time: 126 minutes 16.66 seconds (7576.66 seconds total)