Starting phenix.real_space_refine on Thu Nov 16 20:11:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/11_2023/7n33_24137_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/11_2023/7n33_24137.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/11_2023/7n33_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_24137/11_2023/7n33_24137_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/11_2023/7n33_24137_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/11_2023/7n33_24137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/11_2023/7n33_24137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/11_2023/7n33_24137_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n33_24137/11_2023/7n33_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 15 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: 15 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: 15 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: 15 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: 15 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: 15 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: 8.53, per 1000 atoms: 0.52 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: 6.50 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: 3.83 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: 4.70 Time building geometry restraints manager: 7.02 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: 9804 29.43 - 58.86: 210 58.86 - 88.29: 30 88.29 - 117.72: 6 117.72 - 147.15: 6 Dihedral angle restraints: 10056 sinusoidal: 4032 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 10053 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.160 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 45.870 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.830 ------------------------------------------------------------------------------- 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 : 13.923 147.153 6168 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 *********************** 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 : 2.069 Fit side-chains outliers start: 54 outliers final: 24 residues processed: 323 average time/residue: 1.3440 time to fit residues: 480.3195 Evaluate side-chains 197 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 1.858 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 1.7662 time to fit residues: 8.2109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 159 optimal weight: 7.9990 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: 5.4086 ------------------------------------------------------------------------------- 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: 0.8457 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16872 Z= 0.238 Angle : 0.566 9.672 22902 Z= 0.288 Chirality : 0.050 0.381 2634 Planarity : 0.003 0.022 2922 Dihedral : 9.867 156.814 2238 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.23 % Allowed : 10.69 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2064 helix: 0.60 (0.23), residues: 534 sheet: 1.03 (0.29), residues: 318 loop : 0.11 (0.17), residues: 1212 *********************** 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 250 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 172 time to evaluate : 2.014 Fit side-chains outliers start: 78 outliers final: 32 residues processed: 231 average time/residue: 1.2707 time to fit residues: 327.3765 Evaluate side-chains 186 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 1.951 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 24 residues processed: 8 average time/residue: 0.1573 time to fit residues: 4.8970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 0.0470 chunk 154 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 185 optimal weight: 7.9990 chunk 200 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 63 optimal weight: 30.0000 chunk 148 optimal weight: 9.9990 overall best weight: 4.8086 ------------------------------------------------------------------------------- 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** E 338 HIS ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16872 Z= 0.215 Angle : 0.542 8.532 22902 Z= 0.278 Chirality : 0.050 0.382 2634 Planarity : 0.003 0.023 2922 Dihedral : 10.051 164.235 2238 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.29 % Allowed : 12.21 % Favored : 83.50 % 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: 0.51 (0.18), residues: 2064 helix: 0.64 (0.23), residues: 534 sheet: 0.98 (0.30), residues: 318 loop : 0.11 (0.17), residues: 1212 *********************** 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 241 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 162 time to evaluate : 1.913 Fit side-chains outliers start: 79 outliers final: 35 residues processed: 222 average time/residue: 1.2795 time to fit residues: 317.0327 Evaluate side-chains 187 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 152 time to evaluate : 1.923 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 26 residues processed: 9 average time/residue: 0.6351 time to fit residues: 9.4299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 96 optimal weight: 30.0000 chunk 20 optimal weight: 30.0000 chunk 88 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 176 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** E 338 HIS ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16872 Z= 0.238 Angle : 0.547 8.344 22902 Z= 0.282 Chirality : 0.050 0.383 2634 Planarity : 0.003 0.023 2922 Dihedral : 10.120 165.327 2238 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.64 % Allowed : 13.19 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2064 helix: 0.58 (0.23), residues: 534 sheet: 0.96 (0.29), residues: 318 loop : 0.07 (0.17), residues: 1212 *********************** 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 230 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 163 time to evaluate : 2.118 Fit side-chains outliers start: 67 outliers final: 39 residues processed: 213 average time/residue: 1.2526 time to fit residues: 299.4292 Evaluate side-chains 192 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 1.950 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 30 residues processed: 9 average time/residue: 0.3430 time to fit residues: 6.8123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 49 optimal weight: 40.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16872 Z= 0.257 Angle : 0.554 8.232 22902 Z= 0.286 Chirality : 0.050 0.384 2634 Planarity : 0.003 0.025 2922 Dihedral : 10.212 166.507 2238 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.91 % Allowed : 13.68 % Favored : 82.41 % 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: 0.37 (0.18), residues: 2064 helix: 0.51 (0.23), residues: 534 sheet: 0.99 (0.29), residues: 318 loop : 0.01 (0.17), residues: 1212 *********************** 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 232 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 160 time to evaluate : 2.034 Fit side-chains outliers start: 72 outliers final: 41 residues processed: 217 average time/residue: 1.1840 time to fit residues: 289.0643 Evaluate side-chains 198 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 157 time to evaluate : 2.024 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 32 residues processed: 10 average time/residue: 0.4961 time to fit residues: 9.0711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 30.0000 chunk 177 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 48 optimal weight: 30.0000 chunk 197 optimal weight: 6.9990 chunk 163 optimal weight: 0.5980 chunk 91 optimal weight: 50.0000 chunk 16 optimal weight: 10.0000 chunk 65 optimal weight: 50.0000 chunk 103 optimal weight: 6.9990 overall best weight: 5.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2119 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= 0.222 Angle : 0.545 8.181 22902 Z= 0.281 Chirality : 0.050 0.383 2634 Planarity : 0.003 0.025 2922 Dihedral : 10.170 166.952 2238 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.09 % Allowed : 14.93 % Favored : 81.98 % 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: 0.41 (0.18), residues: 2064 helix: 0.55 (0.23), residues: 534 sheet: 1.03 (0.30), residues: 318 loop : 0.02 (0.17), residues: 1212 *********************** 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 216 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 159 time to evaluate : 2.028 Fit side-chains outliers start: 57 outliers final: 40 residues processed: 209 average time/residue: 1.2681 time to fit residues: 296.4629 Evaluate side-chains 190 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 150 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 35 residues processed: 6 average time/residue: 0.3221 time to fit residues: 5.1880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 29 ASN ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16872 Z= 0.200 Angle : 0.537 8.145 22902 Z= 0.277 Chirality : 0.049 0.381 2634 Planarity : 0.003 0.025 2922 Dihedral : 10.132 167.392 2238 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.37 % Allowed : 14.82 % Favored : 81.81 % 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: 0.43 (0.18), residues: 2064 helix: 0.60 (0.23), residues: 534 sheet: 1.04 (0.30), residues: 318 loop : 0.02 (0.17), residues: 1212 *********************** 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 217 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 155 time to evaluate : 1.909 Fit side-chains outliers start: 62 outliers final: 37 residues processed: 206 average time/residue: 1.2346 time to fit residues: 285.4964 Evaluate side-chains 192 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 155 time to evaluate : 1.764 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 32 residues processed: 5 average time/residue: 0.1639 time to fit residues: 3.9898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 125 optimal weight: 20.0000 chunk 133 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN B 310 GLN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16872 Z= 0.311 Angle : 0.596 10.175 22902 Z= 0.306 Chirality : 0.051 0.387 2634 Planarity : 0.003 0.026 2922 Dihedral : 10.316 166.931 2238 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.64 % Allowed : 14.82 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.26 (0.18), residues: 2064 helix: 0.41 (0.23), residues: 534 sheet: 0.80 (0.30), residues: 318 loop : -0.02 (0.17), residues: 1212 *********************** 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 225 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 158 time to evaluate : 1.954 Fit side-chains outliers start: 67 outliers final: 42 residues processed: 211 average time/residue: 1.2211 time to fit residues: 289.1367 Evaluate side-chains 191 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 149 time to evaluate : 1.986 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 33 residues processed: 9 average time/residue: 0.5531 time to fit residues: 8.8380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 183 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 143 optimal weight: 0.0870 chunk 56 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 164 ASN A 310 GLN B 164 ASN C 164 ASN C 310 GLN 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** E 338 HIS F 310 GLN F 338 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16872 Z= 0.121 Angle : 0.523 12.609 22902 Z= 0.266 Chirality : 0.048 0.376 2634 Planarity : 0.003 0.028 2922 Dihedral : 9.880 167.317 2238 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.12 % Allowed : 16.67 % 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: 0.61 (0.18), residues: 2064 helix: 0.70 (0.23), residues: 540 sheet: 1.14 (0.31), residues: 306 loop : 0.18 (0.17), residues: 1218 *********************** 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 214 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 175 time to evaluate : 2.155 Fit side-chains outliers start: 39 outliers final: 30 residues processed: 212 average time/residue: 1.1850 time to fit residues: 285.5284 Evaluate side-chains 185 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 1.926 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 1 average time/residue: 1.2074 time to fit residues: 3.9441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 91 optimal weight: 0.0770 chunk 134 optimal weight: 20.0000 chunk 203 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 125 optimal weight: 20.0000 chunk 99 optimal weight: 50.0000 chunk 128 optimal weight: 6.9990 overall best weight: 6.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN B 29 ASN B 164 ASN B 310 GLN C 29 ASN 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 338 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2267 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 : 0.593 13.287 22902 Z= 0.300 Chirality : 0.050 0.384 2634 Planarity : 0.003 0.030 2922 Dihedral : 10.177 166.290 2238 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.01 % Allowed : 17.21 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 2064 helix: 0.63 (0.23), residues: 534 sheet: 1.27 (0.31), residues: 282 loop : 0.14 (0.17), residues: 1248 ********************** 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 195 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 2.094 Fit side-chains outliers start: 37 outliers final: 32 residues processed: 194 average time/residue: 1.2647 time to fit residues: 275.1540 Evaluate side-chains 182 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.825 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 1 average time/residue: 0.1860 time to fit residues: 3.8029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 149 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 162 optimal weight: 20.0000 chunk 67 optimal weight: 0.0000 chunk 166 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 30.0000 chunk 142 optimal weight: 5.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 GLN B 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 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.139396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.098982 restraints weight = 21652.777| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.78 r_work: 0.3178 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16872 Z= 0.246 Angle : 0.597 13.782 22902 Z= 0.302 Chirality : 0.050 0.384 2634 Planarity : 0.003 0.032 2922 Dihedral : 10.204 165.459 2238 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.66 % Allowed : 16.50 % Favored : 80.84 % 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: 0.49 (0.18), residues: 2064 helix: 0.54 (0.23), residues: 534 sheet: 1.18 (0.31), residues: 282 loop : 0.12 (0.17), residues: 1248 =============================================================================== Job complete usr+sys time: 6665.64 seconds wall clock time: 119 minutes 6.75 seconds (7146.75 seconds total)