Starting phenix.real_space_refine on Fri Mar 22 06:55:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffi_29043/03_2024/8ffi_29043_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffi_29043/03_2024/8ffi_29043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffi_29043/03_2024/8ffi_29043.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffi_29043/03_2024/8ffi_29043.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffi_29043/03_2024/8ffi_29043_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ffi_29043/03_2024/8ffi_29043_neut.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.106 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 164 5.49 5 Mg 4 5.21 5 S 88 5.16 5 C 20456 2.51 5 N 5416 2.21 5 O 6412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3494 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 406} Chain: "B" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "C" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 9, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 19} Chain: "D" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3494 Classifications: {'peptide': 419} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 406} Chain: "F" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna3p': 20} Chain: "H" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "I" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3494 Classifications: {'peptide': 419} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 406} Chain: "J" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "K" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "L" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "M" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3494 Classifications: {'peptide': 419} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 406} Chain: "N" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "O" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "P" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.91, per 1000 atoms: 0.49 Number of scatterers: 32540 At special positions: 0 Unit cell: (222.3, 131.1, 168.15, 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 88 16.00 P 164 15.00 Mg 4 11.99 O 6412 8.00 N 5416 7.00 C 20456 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: 12.36 Conformation dependent library (CDL) restraints added in 5.3 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6768 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 39 sheets defined 35.4% alpha, 20.5% beta 34 base pairs and 121 stacking pairs defined. Time for finding SS restraints: 10.83 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 71 through 88 Processing helix chain 'A' and resid 123 through 139 removed outlier: 3.918A pdb=" N GLY A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 158 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 257 through 280 Processing helix chain 'A' and resid 300 through 304 removed outlier: 3.562A pdb=" N ASP A 303 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 365 Processing helix chain 'A' and resid 369 through 384 removed outlier: 3.597A pdb=" N LEU A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 22 through 30 Processing helix chain 'B' and resid 46 through 60 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.623A pdb=" N ILE B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 131 removed outlier: 3.683A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 removed outlier: 3.689A pdb=" N TYR B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS B 151 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.619A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 230' Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 331 through 351 Processing helix chain 'B' and resid 366 through 375 Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.627A pdb=" N THR B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 removed outlier: 3.833A pdb=" N ALA B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'E' and resid 14 through 29 Processing helix chain 'E' and resid 34 through 39 removed outlier: 3.694A pdb=" N LEU E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 71 through 89 Processing helix chain 'E' and resid 109 through 114 removed outlier: 4.604A pdb=" N ARG E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 138 Processing helix chain 'E' and resid 149 through 157 removed outlier: 3.569A pdb=" N ILE E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.552A pdb=" N THR E 238 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 249 Processing helix chain 'E' and resid 257 through 280 Processing helix chain 'E' and resid 300 through 302 No H-bonds generated for 'chain 'E' and resid 300 through 302' Processing helix chain 'E' and resid 353 through 365 Processing helix chain 'E' and resid 369 through 384 removed outlier: 3.712A pdb=" N LEU E 384 " --> pdb=" O PHE E 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 22 through 28 Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 77 through 83 Processing helix chain 'F' and resid 97 through 105 removed outlier: 3.828A pdb=" N ILE F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 131 removed outlier: 3.678A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 150 Processing helix chain 'F' and resid 205 through 214 removed outlier: 3.609A pdb=" N LEU F 214 " --> pdb=" O PHE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 248 through 264 Processing helix chain 'F' and resid 331 through 351 Processing helix chain 'F' and resid 366 through 376 removed outlier: 3.636A pdb=" N TRP F 370 " --> pdb=" O ASN F 366 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 462 Processing helix chain 'F' and resid 477 through 480 Processing helix chain 'F' and resid 481 through 490 Processing helix chain 'F' and resid 502 through 506 removed outlier: 3.833A pdb=" N TYR F 505 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 29 Processing helix chain 'I' and resid 44 through 56 Processing helix chain 'I' and resid 71 through 89 Processing helix chain 'I' and resid 123 through 139 Processing helix chain 'I' and resid 149 through 157 removed outlier: 3.724A pdb=" N ILE I 157 " --> pdb=" O LEU I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 203 Processing helix chain 'I' and resid 243 through 247 Processing helix chain 'I' and resid 257 through 279 Processing helix chain 'I' and resid 300 through 304 Processing helix chain 'I' and resid 353 through 366 Processing helix chain 'I' and resid 369 through 385 Processing helix chain 'L' and resid 15 through 17 No H-bonds generated for 'chain 'L' and resid 15 through 17' Processing helix chain 'L' and resid 22 through 30 Processing helix chain 'L' and resid 46 through 60 Processing helix chain 'L' and resid 77 through 83 Processing helix chain 'L' and resid 97 through 105 removed outlier: 3.788A pdb=" N ILE L 101 " --> pdb=" O THR L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 131 removed outlier: 4.154A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE L 125 " --> pdb=" O PHE L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 149 removed outlier: 3.642A pdb=" N TYR L 148 " --> pdb=" O PRO L 144 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 144 through 149' Processing helix chain 'L' and resid 205 through 214 removed outlier: 3.632A pdb=" N LEU L 214 " --> pdb=" O PHE L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 230 Processing helix chain 'L' and resid 248 through 264 Processing helix chain 'L' and resid 331 through 351 removed outlier: 3.690A pdb=" N ALA L 337 " --> pdb=" O LYS L 333 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU L 338 " --> pdb=" O GLU L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 371 Processing helix chain 'L' and resid 451 through 462 Processing helix chain 'L' and resid 481 through 491 Processing helix chain 'L' and resid 502 through 506 removed outlier: 3.753A pdb=" N TYR L 505 " --> pdb=" O ALA L 502 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 28 Processing helix chain 'M' and resid 46 through 56 Processing helix chain 'M' and resid 71 through 89 Processing helix chain 'M' and resid 104 through 108 removed outlier: 3.866A pdb=" N ILE M 108 " --> pdb=" O TYR M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 138 Processing helix chain 'M' and resid 146 through 158 removed outlier: 4.204A pdb=" N SER M 150 " --> pdb=" O ASP M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 203 removed outlier: 3.549A pdb=" N LEU M 203 " --> pdb=" O VAL M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 236 No H-bonds generated for 'chain 'M' and resid 234 through 236' Processing helix chain 'M' and resid 243 through 249 Processing helix chain 'M' and resid 257 through 280 Processing helix chain 'M' and resid 300 through 302 No H-bonds generated for 'chain 'M' and resid 300 through 302' Processing helix chain 'M' and resid 353 through 365 Processing helix chain 'M' and resid 369 through 384 removed outlier: 3.800A pdb=" N LEU M 384 " --> pdb=" O PHE M 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 17 No H-bonds generated for 'chain 'N' and resid 15 through 17' Processing helix chain 'N' and resid 22 through 30 Processing helix chain 'N' and resid 46 through 60 Processing helix chain 'N' and resid 77 through 83 Processing helix chain 'N' and resid 97 through 103 removed outlier: 3.819A pdb=" N LYS N 103 " --> pdb=" O GLU N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 131 removed outlier: 4.111A pdb=" N LYS N 124 " --> pdb=" O LEU N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 151 removed outlier: 3.619A pdb=" N TYR N 148 " --> pdb=" O PRO N 144 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR N 150 " --> pdb=" O GLU N 146 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 214 removed outlier: 3.605A pdb=" N LEU N 214 " --> pdb=" O PHE N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 230 removed outlier: 3.541A pdb=" N ALA N 230 " --> pdb=" O GLU N 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 226 through 230' Processing helix chain 'N' and resid 248 through 264 Processing helix chain 'N' and resid 331 through 351 Processing helix chain 'N' and resid 366 through 376 removed outlier: 3.756A pdb=" N VAL N 376 " --> pdb=" O ALA N 372 " (cutoff:3.500A) Processing helix chain 'N' and resid 451 through 462 Processing helix chain 'N' and resid 463 through 465 No H-bonds generated for 'chain 'N' and resid 463 through 465' Processing helix chain 'N' and resid 481 through 490 Processing helix chain 'N' and resid 502 through 506 removed outlier: 3.688A pdb=" N TYR N 505 " --> pdb=" O ALA N 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.080A pdb=" N ILE A 5 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LYS A 4 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE A 60 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 6 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU A 62 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER A 8 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER A 64 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N ILE A 118 " --> pdb=" O ILE A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 3 removed outlier: 4.391A pdb=" N LYS A 409 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR A 171 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS A 411 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU A 169 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN A 413 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 177 removed outlier: 5.065A pdb=" N GLY A 325 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N THR A 291 " --> pdb=" O GLY A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 210 removed outlier: 3.529A pdb=" N TYR A 210 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 390 through 394 Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 6 removed outlier: 6.662A pdb=" N SER B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY B 385 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN B 296 " --> pdb=" O TRP B 320 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP B 320 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS B 298 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLY B 318 " --> pdb=" O CYS B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AA9, first strand: chain 'B' and resid 91 through 95 removed outlier: 6.578A pdb=" N GLY B 42 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE B 142 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 44 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 425 through 426 removed outlier: 3.546A pdb=" N THR B 431 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 32 through 33 removed outlier: 6.491A pdb=" N ILE E 5 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHE E 6 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL E 63 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER E 8 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE E 60 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU E 97 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU E 62 " --> pdb=" O LEU E 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 311 through 315 removed outlier: 4.555A pdb=" N LEU F 305 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL F 278 " --> pdb=" O LEU F 305 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N CYS F 279 " --> pdb=" O PHE F 358 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N HIS F 360 " --> pdb=" O CYS F 279 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU F 281 " --> pdb=" O HIS F 360 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS F 447 " --> pdb=" O GLY F 385 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR F 387 " --> pdb=" O ILE F 445 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE F 445 " --> pdb=" O THR F 387 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N SER F 389 " --> pdb=" O ILE F 443 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE F 443 " --> pdb=" O SER F 389 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL F 412 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU F 3 " --> pdb=" O VAL F 412 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS E 411 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N TYR F 6 " --> pdb=" O LYS E 411 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 283 through 286 removed outlier: 7.336A pdb=" N THR E 291 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY E 325 " --> pdb=" O THR E 291 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 283 through 286 removed outlier: 7.336A pdb=" N THR E 291 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY E 325 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU E 176 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER E 177 " --> pdb=" O SER E 404 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE E 402 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 208 through 210 Processing sheet with id=AB7, first strand: chain 'E' and resid 304 through 305 Processing sheet with id=AB8, first strand: chain 'F' and resid 12 through 13 Processing sheet with id=AB9, first strand: chain 'F' and resid 93 through 95 removed outlier: 8.414A pdb=" N LYS F 94 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL F 43 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY F 42 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE F 142 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE F 44 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP F 139 " --> pdb=" O GLN F 222 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE F 224 " --> pdb=" O TRP F 139 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL F 141 " --> pdb=" O PHE F 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 284 through 286 removed outlier: 3.539A pdb=" N TRP F 320 " --> pdb=" O CYS F 298 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 425 through 426 removed outlier: 3.660A pdb=" N THR F 431 " --> pdb=" O VAL F 426 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 32 through 33 removed outlier: 6.368A pdb=" N ILE I 5 " --> pdb=" O TRP I 33 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE I 6 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL I 63 " --> pdb=" O PHE I 6 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N SER I 8 " --> pdb=" O VAL I 63 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 310 through 316 removed outlier: 3.634A pdb=" N GLY L 310 " --> pdb=" O ASP L 306 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG L 295 " --> pdb=" O VAL L 288 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU L 305 " --> pdb=" O VAL L 278 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL L 278 " --> pdb=" O LEU L 305 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL L 357 " --> pdb=" O VAL L 384 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL L 386 " --> pdb=" O VAL L 357 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE L 359 " --> pdb=" O VAL L 386 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE L 388 " --> pdb=" O ILE L 359 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ALA L 361 " --> pdb=" O ILE L 388 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY L 385 " --> pdb=" O ASN L 446 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL L 412 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU L 3 " --> pdb=" O VAL L 412 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN I 413 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N TYR L 6 " --> pdb=" O ASN I 413 " (cutoff:3.500A) removed outlier: 10.165A pdb=" N SER I 415 " --> pdb=" O TYR L 6 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL I 414 " --> pdb=" O LYS I 167 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LYS I 167 " --> pdb=" O VAL I 414 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 283 through 286 removed outlier: 7.014A pdb=" N THR I 291 " --> pdb=" O GLY I 325 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLY I 325 " --> pdb=" O THR I 291 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 283 through 286 removed outlier: 7.014A pdb=" N THR I 291 " --> pdb=" O GLY I 325 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLY I 325 " --> pdb=" O THR I 291 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N SER I 177 " --> pdb=" O SER I 404 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE I 402 " --> pdb=" O LEU I 179 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 207 through 210 Processing sheet with id=AC8, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AC9, first strand: chain 'L' and resid 92 through 95 removed outlier: 6.915A pdb=" N SER L 41 " --> pdb=" O THR L 92 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LYS L 94 " --> pdb=" O SER L 41 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL L 43 " --> pdb=" O LYS L 94 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY L 42 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE L 142 " --> pdb=" O GLY L 42 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE L 44 " --> pdb=" O ILE L 142 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 425 through 426 Processing sheet with id=AD2, first strand: chain 'M' and resid 32 through 33 removed outlier: 6.447A pdb=" N ILE M 5 " --> pdb=" O TRP M 33 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE M 60 " --> pdb=" O ILE M 95 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU M 97 " --> pdb=" O PHE M 60 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU M 62 " --> pdb=" O LEU M 97 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 2 through 3 removed outlier: 4.091A pdb=" N VAL M 414 " --> pdb=" O LYS M 167 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LYS M 167 " --> pdb=" O VAL M 414 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 283 through 286 removed outlier: 6.953A pdb=" N THR M 291 " --> pdb=" O GLY M 325 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY M 325 " --> pdb=" O THR M 291 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 283 through 286 removed outlier: 6.953A pdb=" N THR M 291 " --> pdb=" O GLY M 325 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY M 325 " --> pdb=" O THR M 291 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER M 324 " --> pdb=" O SER M 338 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N SER M 177 " --> pdb=" O SER M 404 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE M 402 " --> pdb=" O LEU M 179 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 208 through 210 Processing sheet with id=AD7, first strand: chain 'M' and resid 304 through 305 Processing sheet with id=AD8, first strand: chain 'N' and resid 5 through 6 removed outlier: 6.666A pdb=" N GLY N 385 " --> pdb=" O ASN N 446 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL N 357 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL N 386 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE N 359 " --> pdb=" O VAL N 386 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE N 388 " --> pdb=" O ILE N 359 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA N 361 " --> pdb=" O ILE N 388 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N CYS N 279 " --> pdb=" O PHE N 358 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N HIS N 360 " --> pdb=" O CYS N 279 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU N 281 " --> pdb=" O HIS N 360 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 5 through 6 removed outlier: 6.666A pdb=" N GLY N 385 " --> pdb=" O ASN N 446 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL N 357 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL N 386 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE N 359 " --> pdb=" O VAL N 386 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE N 388 " --> pdb=" O ILE N 359 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA N 361 " --> pdb=" O ILE N 388 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N CYS N 279 " --> pdb=" O PHE N 358 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N HIS N 360 " --> pdb=" O CYS N 279 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU N 281 " --> pdb=" O HIS N 360 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AE2, first strand: chain 'N' and resid 92 through 95 removed outlier: 6.318A pdb=" N GLY N 42 " --> pdb=" O PHE N 140 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE N 142 " --> pdb=" O GLY N 42 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE N 44 " --> pdb=" O ILE N 142 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TRP N 139 " --> pdb=" O GLN N 222 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE N 224 " --> pdb=" O TRP N 139 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL N 141 " --> pdb=" O PHE N 224 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 425 through 426 1203 hydrogen bonds defined for protein. 3363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 85 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 121 stacking parallelities Total time for adding SS restraints: 12.04 Time building geometry restraints manager: 13.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6272 1.33 - 1.45: 9074 1.45 - 1.57: 17878 1.57 - 1.69: 320 1.69 - 1.81: 132 Bond restraints: 33676 Sorted by residual: bond pdb=" C3' DC P 4 " pdb=" O3' DC P 4 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" C3' DC K 22 " pdb=" O3' DC K 22 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 2.00e+00 bond pdb=" C3' DG H 15 " pdb=" O3' DG H 15 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.75e+00 bond pdb=" C3' DT D 12 " pdb=" O3' DT D 12 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.72e+00 bond pdb=" C3' DG D 15 " pdb=" O3' DG D 15 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.68e+00 ... (remaining 33671 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.97: 1753 106.97 - 114.34: 19517 114.34 - 121.71: 17182 121.71 - 129.08: 7465 129.08 - 136.45: 339 Bond angle restraints: 46256 Sorted by residual: angle pdb=" C ASP B 306 " pdb=" N ASN B 307 " pdb=" CA ASN B 307 " ideal model delta sigma weight residual 126.45 136.45 -10.00 1.77e+00 3.19e-01 3.19e+01 angle pdb=" C LYS E 211 " pdb=" CA LYS E 211 " pdb=" CB LYS E 211 " ideal model delta sigma weight residual 115.89 110.96 4.93 1.32e+00 5.74e-01 1.39e+01 angle pdb=" N GLY B 318 " pdb=" CA GLY B 318 " pdb=" C GLY B 318 " ideal model delta sigma weight residual 112.34 105.15 7.19 2.04e+00 2.40e-01 1.24e+01 angle pdb=" O4' A J 11 " pdb=" C1' A J 11 " pdb=" N9 A J 11 " ideal model delta sigma weight residual 108.20 113.22 -5.02 1.50e+00 4.44e-01 1.12e+01 angle pdb=" C SER E 68 " pdb=" N ASN E 69 " pdb=" CA ASN E 69 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 ... (remaining 46251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 19333 35.84 - 71.68: 659 71.68 - 107.51: 34 107.51 - 143.35: 1 143.35 - 179.19: 21 Dihedral angle restraints: 20048 sinusoidal: 9572 harmonic: 10476 Sorted by residual: dihedral pdb=" O4' U G 13 " pdb=" C1' U G 13 " pdb=" N1 U G 13 " pdb=" C2 U G 13 " ideal model delta sinusoidal sigma weight residual 200.00 20.81 179.19 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U O 17 " pdb=" C1' U O 17 " pdb=" N1 U O 17 " pdb=" C2 U O 17 " ideal model delta sinusoidal sigma weight residual -160.00 19.03 -179.03 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U C 13 " pdb=" C1' U C 13 " pdb=" N1 U C 13 " pdb=" C2 U C 13 " ideal model delta sinusoidal sigma weight residual -160.00 17.31 -177.31 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 20045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 4070 0.049 - 0.099: 775 0.099 - 0.148: 222 0.148 - 0.197: 8 0.197 - 0.247: 1 Chirality restraints: 5076 Sorted by residual: chirality pdb=" CB ILE I 157 " pdb=" CA ILE I 157 " pdb=" CG1 ILE I 157 " pdb=" CG2 ILE I 157 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CB ILE M 418 " pdb=" CA ILE M 418 " pdb=" CG1 ILE M 418 " pdb=" CG2 ILE M 418 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.25e-01 chirality pdb=" CB ILE A 418 " pdb=" CA ILE A 418 " pdb=" CG1 ILE A 418 " pdb=" CG2 ILE A 418 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.99e-01 ... (remaining 5073 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 33 " 0.022 2.00e-02 2.50e+03 2.29e-02 1.31e+01 pdb=" CG TRP M 33 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP M 33 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP M 33 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP M 33 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP M 33 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP M 33 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 33 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 33 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP M 33 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A O 11 " -0.034 2.00e-02 2.50e+03 1.69e-02 7.83e+00 pdb=" N9 A O 11 " 0.043 2.00e-02 2.50e+03 pdb=" C8 A O 11 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A O 11 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A O 11 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A O 11 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A O 11 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A O 11 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A O 11 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A O 11 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A O 11 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A J 11 " -0.034 2.00e-02 2.50e+03 1.67e-02 7.69e+00 pdb=" N9 A J 11 " 0.042 2.00e-02 2.50e+03 pdb=" C8 A J 11 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A J 11 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A J 11 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A J 11 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A J 11 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A J 11 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A J 11 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A J 11 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A J 11 " 0.001 2.00e-02 2.50e+03 ... (remaining 5261 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 170 2.57 - 3.15: 24229 3.15 - 3.73: 48549 3.73 - 4.32: 71085 4.32 - 4.90: 116374 Nonbonded interactions: 260407 Sorted by model distance: nonbonded pdb=" OP2 U G 1 " pdb="MG MG F 601 " model vdw 1.987 2.170 nonbonded pdb=" OP2 U J 1 " pdb="MG MG L 601 " model vdw 2.067 2.170 nonbonded pdb=" OP1 A G 3 " pdb="MG MG F 601 " model vdw 2.116 2.170 nonbonded pdb=" OG SER B 67 " pdb=" OP1 DA D 23 " model vdw 2.198 2.440 nonbonded pdb=" O GLY F 487 " pdb=" OG1 THR F 491 " model vdw 2.205 2.440 ... (remaining 260402 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 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'K' selection = chain 'P' } 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: 3.190 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: 0.020 Extract box with map and model: 17.370 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 87.280 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.230 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:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.003 0.045 33676 Z= 0.165 Angle : 0.562 10.815 46256 Z= 0.310 Chirality : 0.042 0.247 5076 Planarity : 0.004 0.053 5264 Dihedral : 17.750 179.188 13280 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.88 (0.14), residues: 3528 helix: 1.12 (0.16), residues: 1138 sheet: -0.44 (0.19), residues: 748 loop : -1.92 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP M 33 HIS 0.007 0.001 HIS M 9 PHE 0.037 0.001 PHE M 6 TYR 0.015 0.001 TYR A 221 ARG 0.003 0.000 ARG F 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 3.574 Fit side-chains REVERT: A 129 LYS cc_start: 0.7386 (mttp) cc_final: 0.7164 (mttp) REVERT: A 161 ASP cc_start: 0.7348 (p0) cc_final: 0.7005 (p0) REVERT: E 122 MET cc_start: 0.6456 (mmt) cc_final: 0.6203 (mmt) REVERT: E 189 GLU cc_start: 0.7295 (tt0) cc_final: 0.7073 (tt0) REVERT: F 216 LYS cc_start: 0.6851 (pttm) cc_final: 0.6600 (tptt) REVERT: F 314 LYS cc_start: 0.6738 (ptpp) cc_final: 0.6307 (mmtt) REVERT: I 283 GLN cc_start: 0.7812 (mm110) cc_final: 0.7481 (mp10) REVERT: N 131 ASN cc_start: 0.6782 (m-40) cc_final: 0.6053 (p0) REVERT: N 415 GLU cc_start: 0.6563 (tp30) cc_final: 0.6299 (tp30) outliers start: 0 outliers final: 1 residues processed: 417 average time/residue: 1.6163 time to fit residues: 785.1123 Evaluate side-chains 301 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 300 time to evaluate : 3.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 418 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 0.5980 chunk 275 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 173 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 330 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN B 207 HIS B 296 ASN E 15 ASN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN L 302 GLN M 15 ASN M 370 ASN N 18 GLN N 430 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33676 Z= 0.221 Angle : 0.578 9.485 46256 Z= 0.309 Chirality : 0.043 0.265 5076 Planarity : 0.004 0.052 5264 Dihedral : 18.481 179.733 6030 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.76 % Allowed : 8.84 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.72 (0.14), residues: 3528 helix: 1.33 (0.16), residues: 1146 sheet: -0.37 (0.19), residues: 752 loop : -1.91 (0.14), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 33 HIS 0.004 0.001 HIS M 9 PHE 0.022 0.002 PHE F 14 TYR 0.017 0.001 TYR M 392 ARG 0.007 0.000 ARG L 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 322 time to evaluate : 3.623 Fit side-chains REVERT: A 28 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7267 (mm) REVERT: A 229 LYS cc_start: 0.6798 (ttpt) cc_final: 0.5795 (tmmt) REVERT: B 8 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6710 (mm-30) REVERT: E 122 MET cc_start: 0.6418 (mmt) cc_final: 0.6172 (mmt) REVERT: E 260 GLU cc_start: 0.7320 (tp30) cc_final: 0.7087 (tp30) REVERT: E 299 LYS cc_start: 0.7385 (mtpt) cc_final: 0.7159 (ttpp) REVERT: F 216 LYS cc_start: 0.6983 (pttm) cc_final: 0.6625 (tptt) REVERT: F 314 LYS cc_start: 0.6781 (ptpp) cc_final: 0.6301 (mmtt) REVERT: F 356 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.5629 (mt-10) REVERT: F 453 LYS cc_start: 0.8189 (ttmm) cc_final: 0.7936 (mtmt) REVERT: I 122 MET cc_start: 0.7102 (ptm) cc_final: 0.6829 (ptm) REVERT: I 189 GLU cc_start: 0.7589 (tt0) cc_final: 0.7365 (tt0) REVERT: I 237 LYS cc_start: 0.7421 (ttmm) cc_final: 0.6428 (ttmm) REVERT: I 284 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7477 (pt0) REVERT: L 1 MET cc_start: 0.7856 (tpt) cc_final: 0.7440 (tpt) REVERT: L 48 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.7072 (mm-40) REVERT: L 350 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6248 (mp) REVERT: M 307 LYS cc_start: 0.7451 (mptt) cc_final: 0.7052 (mtpt) REVERT: M 370 ASN cc_start: 0.7437 (t0) cc_final: 0.7229 (t0) REVERT: N 348 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6598 (mt-10) outliers start: 56 outliers final: 28 residues processed: 346 average time/residue: 1.5825 time to fit residues: 639.9737 Evaluate side-chains 334 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 299 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain L residue 48 GLN Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 348 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 357 optimal weight: 0.9990 chunk 294 optimal weight: 0.7980 chunk 328 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 HIS E 191 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 302 GLN M 258 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33676 Z= 0.270 Angle : 0.606 9.668 46256 Z= 0.323 Chirality : 0.044 0.195 5076 Planarity : 0.005 0.054 5264 Dihedral : 18.491 179.300 6028 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.33 % Allowed : 11.54 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.75 (0.14), residues: 3528 helix: 1.32 (0.16), residues: 1146 sheet: -0.37 (0.19), residues: 744 loop : -1.94 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 319 HIS 0.003 0.001 HIS A 160 PHE 0.018 0.002 PHE F 14 TYR 0.017 0.002 TYR A 221 ARG 0.007 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 306 time to evaluate : 3.543 Fit side-chains REVERT: A 28 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7340 (mm) REVERT: A 190 TYR cc_start: 0.7556 (m-10) cc_final: 0.7337 (m-10) REVERT: A 221 TYR cc_start: 0.5626 (p90) cc_final: 0.4915 (p90) REVERT: A 229 LYS cc_start: 0.6847 (ttpt) cc_final: 0.5831 (tmmt) REVERT: A 391 PHE cc_start: 0.6473 (OUTLIER) cc_final: 0.4744 (t80) REVERT: B 8 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6746 (mm-30) REVERT: B 85 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8349 (mtpt) REVERT: E 237 LYS cc_start: 0.6230 (mttt) cc_final: 0.5971 (ttmm) REVERT: E 244 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7400 (pp20) REVERT: E 260 GLU cc_start: 0.7378 (tp30) cc_final: 0.7125 (tp30) REVERT: E 283 GLN cc_start: 0.6961 (mm110) cc_final: 0.6534 (mm-40) REVERT: F 216 LYS cc_start: 0.6994 (pttm) cc_final: 0.6621 (tptt) REVERT: F 356 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5576 (mt-10) REVERT: I 122 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6852 (ptm) REVERT: I 234 HIS cc_start: 0.5857 (t-90) cc_final: 0.5536 (t70) REVERT: I 284 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7454 (pt0) REVERT: L 48 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.7090 (mm-40) REVERT: L 350 ILE cc_start: 0.6804 (OUTLIER) cc_final: 0.6269 (mp) REVERT: L 435 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7233 (mtt) REVERT: M 307 LYS cc_start: 0.7539 (mptt) cc_final: 0.7119 (mtpt) REVERT: M 370 ASN cc_start: 0.7409 (t0) cc_final: 0.7209 (t0) REVERT: N 1 MET cc_start: 0.8252 (tpp) cc_final: 0.7995 (mmm) REVERT: N 8 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: N 348 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6636 (mt-10) REVERT: N 430 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.6913 (mp10) outliers start: 74 outliers final: 37 residues processed: 341 average time/residue: 1.5702 time to fit residues: 627.2210 Evaluate side-chains 336 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 285 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 279 ASP Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain L residue 48 GLN Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 327 GLN Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 430 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 0.0470 chunk 248 optimal weight: 0.2980 chunk 171 optimal weight: 0.0010 chunk 36 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 351 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 314 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 0.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN E 191 ASN E 320 HIS E 364 GLN E 370 ASN F 129 ASN L 302 GLN N 18 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33676 Z= 0.156 Angle : 0.522 10.423 46256 Z= 0.281 Chirality : 0.041 0.287 5076 Planarity : 0.004 0.047 5264 Dihedral : 18.363 179.582 6028 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.04 % Allowed : 12.83 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3528 helix: 1.70 (0.16), residues: 1144 sheet: -0.23 (0.19), residues: 746 loop : -1.82 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 319 HIS 0.003 0.001 HIS E 160 PHE 0.014 0.001 PHE I 158 TYR 0.024 0.001 TYR M 392 ARG 0.009 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 303 time to evaluate : 3.539 Fit side-chains REVERT: A 28 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7296 (mm) REVERT: A 190 TYR cc_start: 0.7523 (m-10) cc_final: 0.7320 (m-10) REVERT: A 221 TYR cc_start: 0.5542 (p90) cc_final: 0.4783 (p90) REVERT: A 224 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7568 (m) REVERT: A 229 LYS cc_start: 0.6835 (ttpt) cc_final: 0.5839 (tmmt) REVERT: A 391 PHE cc_start: 0.6371 (OUTLIER) cc_final: 0.4638 (t80) REVERT: E 237 LYS cc_start: 0.6195 (mttt) cc_final: 0.5930 (ttmm) REVERT: E 244 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7360 (pp20) REVERT: E 260 GLU cc_start: 0.7236 (tp30) cc_final: 0.6871 (tp30) REVERT: E 283 GLN cc_start: 0.6944 (mm110) cc_final: 0.6556 (mm-40) REVERT: E 393 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7626 (mt) REVERT: F 216 LYS cc_start: 0.6975 (pttm) cc_final: 0.6611 (tptt) REVERT: I 183 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: I 234 HIS cc_start: 0.5715 (t-90) cc_final: 0.5445 (t70) REVERT: M 45 PHE cc_start: 0.6208 (t80) cc_final: 0.5810 (t80) REVERT: M 261 CYS cc_start: 0.7329 (OUTLIER) cc_final: 0.7026 (m) REVERT: M 307 LYS cc_start: 0.7511 (mptt) cc_final: 0.7107 (mtpt) REVERT: N 1 MET cc_start: 0.8195 (tpp) cc_final: 0.7901 (mmm) REVERT: N 8 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7436 (mt-10) REVERT: N 348 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6548 (mt-10) outliers start: 65 outliers final: 27 residues processed: 337 average time/residue: 1.5106 time to fit residues: 599.7657 Evaluate side-chains 321 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 285 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 367 ASN Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain N residue 348 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 261 optimal weight: 0.0870 chunk 145 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 243 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 315 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 ASN A 370 ASN B 414 ASN E 191 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 405 ASN L 302 GLN M 3 ASN N 18 GLN N 430 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 33676 Z= 0.391 Angle : 0.686 11.241 46256 Z= 0.363 Chirality : 0.048 0.194 5076 Planarity : 0.005 0.060 5264 Dihedral : 18.541 178.525 6028 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.02 % Allowed : 13.77 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.82 (0.14), residues: 3528 helix: 1.20 (0.16), residues: 1142 sheet: -0.33 (0.19), residues: 730 loop : -1.96 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 192 HIS 0.005 0.001 HIS B 59 PHE 0.023 0.003 PHE I 45 TYR 0.022 0.002 TYR M 392 ARG 0.007 0.001 ARG M 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 302 time to evaluate : 3.564 Fit side-chains REVERT: A 28 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7321 (mm) REVERT: A 189 GLU cc_start: 0.8010 (tt0) cc_final: 0.7805 (tt0) REVERT: A 190 TYR cc_start: 0.7641 (m-10) cc_final: 0.7346 (m-10) REVERT: A 221 TYR cc_start: 0.5604 (p90) cc_final: 0.4718 (p90) REVERT: A 229 LYS cc_start: 0.6772 (ttpt) cc_final: 0.5816 (tmmt) REVERT: A 313 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7872 (tppt) REVERT: A 391 PHE cc_start: 0.6764 (OUTLIER) cc_final: 0.5143 (t80) REVERT: B 8 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6714 (mm-30) REVERT: E 191 ASN cc_start: 0.6705 (m110) cc_final: 0.6296 (m-40) REVERT: E 237 LYS cc_start: 0.6309 (mttt) cc_final: 0.6044 (ttmm) REVERT: E 244 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7385 (pp20) REVERT: E 260 GLU cc_start: 0.7455 (tp30) cc_final: 0.7090 (tp30) REVERT: E 299 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6699 (ttpt) REVERT: E 393 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7818 (mt) REVERT: I 183 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7182 (mt-10) REVERT: I 394 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7083 (mt-10) REVERT: L 327 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7597 (tt0) REVERT: L 350 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6312 (mp) REVERT: L 435 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7179 (mtt) REVERT: M 45 PHE cc_start: 0.6247 (t80) cc_final: 0.5840 (t80) REVERT: M 370 ASN cc_start: 0.7441 (t0) cc_final: 0.7180 (t0) REVERT: N 1 MET cc_start: 0.8204 (tpp) cc_final: 0.7981 (mmm) REVERT: N 8 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: N 275 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7508 (ptt90) REVERT: N 348 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6742 (mt-10) outliers start: 96 outliers final: 46 residues processed: 357 average time/residue: 1.5014 time to fit residues: 629.9646 Evaluate side-chains 342 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 281 time to evaluate : 3.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 MET Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain I residue 394 GLU Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 327 GLN Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain N residue 275 ARG Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 391 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 4.9990 chunk 316 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 206 optimal weight: 0.0870 chunk 86 optimal weight: 1.9990 chunk 352 optimal weight: 0.4980 chunk 292 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN B 414 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN L 302 GLN M 3 ASN M 318 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33676 Z= 0.201 Angle : 0.565 12.240 46256 Z= 0.303 Chirality : 0.043 0.284 5076 Planarity : 0.004 0.053 5264 Dihedral : 18.397 179.256 6028 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.36 % Allowed : 15.44 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3528 helix: 1.51 (0.16), residues: 1140 sheet: -0.28 (0.19), residues: 736 loop : -1.89 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 319 HIS 0.003 0.001 HIS E 160 PHE 0.013 0.002 PHE I 158 TYR 0.019 0.001 TYR A 392 ARG 0.008 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 288 time to evaluate : 3.018 Fit side-chains REVERT: A 28 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7334 (mm) REVERT: A 189 GLU cc_start: 0.7982 (tt0) cc_final: 0.7766 (tt0) REVERT: A 221 TYR cc_start: 0.5448 (p90) cc_final: 0.4643 (p90) REVERT: A 229 LYS cc_start: 0.6833 (ttpt) cc_final: 0.5826 (pptt) REVERT: A 313 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7765 (tppt) REVERT: A 318 ASN cc_start: 0.8180 (m110) cc_final: 0.7879 (m-40) REVERT: A 391 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.4867 (t80) REVERT: B 8 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6709 (mm-30) REVERT: E 86 LYS cc_start: 0.8065 (ttmm) cc_final: 0.7795 (tmmt) REVERT: E 122 MET cc_start: 0.6466 (mmt) cc_final: 0.6138 (mmt) REVERT: E 237 LYS cc_start: 0.6319 (mttt) cc_final: 0.6052 (ttmm) REVERT: E 244 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7436 (pp20) REVERT: E 260 GLU cc_start: 0.7318 (tp30) cc_final: 0.6938 (tp30) REVERT: E 299 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6651 (ttpt) REVERT: E 393 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7717 (mt) REVERT: F 453 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7950 (mtmt) REVERT: I 183 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7154 (mt-10) REVERT: I 229 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7639 (pttp) REVERT: I 234 HIS cc_start: 0.5762 (t-90) cc_final: 0.5510 (t70) REVERT: L 350 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6186 (mp) REVERT: M 45 PHE cc_start: 0.6201 (t80) cc_final: 0.5798 (t80) REVERT: M 307 LYS cc_start: 0.7504 (mptt) cc_final: 0.7149 (mppt) REVERT: N 1 MET cc_start: 0.8237 (tpp) cc_final: 0.7926 (mmm) REVERT: N 8 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7463 (mt-10) REVERT: N 275 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7522 (ptt90) REVERT: N 348 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6603 (mt-10) outliers start: 75 outliers final: 43 residues processed: 336 average time/residue: 1.5110 time to fit residues: 598.6595 Evaluate side-chains 334 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 279 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 273 ASP Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 350 ILE Chi-restraints excluded: chain L residue 449 GLU Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 194 LEU Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain N residue 275 ARG Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 391 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 257 optimal weight: 0.6980 chunk 199 optimal weight: 0.9980 chunk 296 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 350 optimal weight: 0.0970 chunk 219 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 ASN M 3 ASN M 318 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33676 Z= 0.166 Angle : 0.534 14.271 46256 Z= 0.285 Chirality : 0.041 0.326 5076 Planarity : 0.004 0.048 5264 Dihedral : 18.298 179.730 6028 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.02 % Rotamer: Outliers : 2.26 % Allowed : 15.94 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.39 (0.14), residues: 3528 helix: 1.75 (0.16), residues: 1140 sheet: -0.17 (0.19), residues: 736 loop : -1.82 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 319 HIS 0.003 0.001 HIS F 217 PHE 0.014 0.001 PHE F 14 TYR 0.026 0.001 TYR M 392 ARG 0.009 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 297 time to evaluate : 3.609 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7331 (mm) REVERT: A 133 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6829 (mm-30) REVERT: A 221 TYR cc_start: 0.5423 (p90) cc_final: 0.4598 (p90) REVERT: A 229 LYS cc_start: 0.6772 (ttpt) cc_final: 0.5772 (pptt) REVERT: A 313 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7757 (tppt) REVERT: A 318 ASN cc_start: 0.8127 (m110) cc_final: 0.7749 (m-40) REVERT: A 391 PHE cc_start: 0.6349 (OUTLIER) cc_final: 0.4620 (t80) REVERT: B 1 MET cc_start: 0.8505 (tpt) cc_final: 0.8196 (tpt) REVERT: E 86 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7850 (tmmt) REVERT: E 122 MET cc_start: 0.6373 (mmt) cc_final: 0.6078 (mmt) REVERT: E 237 LYS cc_start: 0.6218 (mttt) cc_final: 0.5962 (ttmm) REVERT: E 244 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7424 (pp20) REVERT: E 260 GLU cc_start: 0.7238 (tp30) cc_final: 0.6873 (tp30) REVERT: E 299 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.6597 (ttpt) REVERT: I 183 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7136 (mt-10) REVERT: I 234 HIS cc_start: 0.5614 (t-90) cc_final: 0.5335 (t70) REVERT: I 284 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: M 45 PHE cc_start: 0.6313 (t80) cc_final: 0.5926 (t80) REVERT: M 261 CYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6985 (m) REVERT: M 307 LYS cc_start: 0.7459 (mptt) cc_final: 0.7124 (mppt) REVERT: N 1 MET cc_start: 0.8240 (tpp) cc_final: 0.7954 (mmm) REVERT: N 8 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: N 275 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7540 (ptt90) REVERT: N 348 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6526 (mt-10) outliers start: 72 outliers final: 38 residues processed: 341 average time/residue: 1.5041 time to fit residues: 604.3577 Evaluate side-chains 336 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 286 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 273 ASP Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 449 GLU Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain N residue 275 ARG Chi-restraints excluded: chain N residue 348 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 275 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33676 Z= 0.271 Angle : 0.612 13.646 46256 Z= 0.324 Chirality : 0.044 0.264 5076 Planarity : 0.005 0.053 5264 Dihedral : 18.358 179.702 6028 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.75 % Favored : 93.23 % Rotamer: Outliers : 2.48 % Allowed : 16.35 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.55 (0.14), residues: 3528 helix: 1.52 (0.16), residues: 1142 sheet: -0.24 (0.19), residues: 746 loop : -1.87 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 319 HIS 0.003 0.001 HIS A 160 PHE 0.017 0.002 PHE I 45 TYR 0.025 0.002 TYR A 392 ARG 0.008 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 291 time to evaluate : 3.570 Fit side-chains REVERT: A 28 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7333 (mm) REVERT: A 221 TYR cc_start: 0.5621 (p90) cc_final: 0.4817 (p90) REVERT: A 229 LYS cc_start: 0.6773 (ttpt) cc_final: 0.5777 (pptt) REVERT: A 313 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7737 (tppt) REVERT: A 318 ASN cc_start: 0.8225 (m110) cc_final: 0.7868 (m-40) REVERT: A 391 PHE cc_start: 0.6678 (OUTLIER) cc_final: 0.5023 (t80) REVERT: B 8 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6706 (mm-30) REVERT: E 122 MET cc_start: 0.6498 (mmt) cc_final: 0.6165 (mmt) REVERT: E 237 LYS cc_start: 0.6293 (mttt) cc_final: 0.6026 (ttmm) REVERT: E 244 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: E 257 ARG cc_start: 0.7071 (mmm-85) cc_final: 0.6847 (mmm-85) REVERT: E 260 GLU cc_start: 0.7368 (tp30) cc_final: 0.7074 (tp30) REVERT: E 299 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6665 (ttpt) REVERT: F 348 GLU cc_start: 0.6379 (pp20) cc_final: 0.6052 (pp20) REVERT: I 183 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7166 (mt-10) REVERT: I 193 MET cc_start: 0.4298 (tmt) cc_final: 0.3556 (tmm) REVERT: I 229 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7766 (pttp) REVERT: I 234 HIS cc_start: 0.5687 (t-90) cc_final: 0.5458 (t70) REVERT: I 284 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: L 327 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: M 307 LYS cc_start: 0.7561 (mptt) cc_final: 0.7186 (mppt) REVERT: N 1 MET cc_start: 0.8200 (tpp) cc_final: 0.7907 (mmm) REVERT: N 8 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: N 275 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7532 (ptt90) REVERT: N 348 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6666 (mt-10) outliers start: 79 outliers final: 50 residues processed: 344 average time/residue: 1.5252 time to fit residues: 615.8291 Evaluate side-chains 344 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 282 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 402 ASP Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 273 ASP Chi-restraints excluded: chain L residue 296 ASN Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 327 GLN Chi-restraints excluded: chain L residue 339 LEU Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 449 GLU Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain N residue 275 ARG Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 391 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 0.9990 chunk 336 optimal weight: 0.7980 chunk 306 optimal weight: 0.6980 chunk 326 optimal weight: 0.6980 chunk 196 optimal weight: 0.0570 chunk 142 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 295 optimal weight: 1.9990 chunk 309 optimal weight: 0.8980 chunk 325 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN E 138 GLN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 ASN L 296 ASN M 3 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33676 Z= 0.173 Angle : 0.548 15.370 46256 Z= 0.292 Chirality : 0.042 0.267 5076 Planarity : 0.004 0.047 5264 Dihedral : 18.266 179.771 6028 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.78 % Favored : 94.19 % Rotamer: Outliers : 2.20 % Allowed : 17.01 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.36 (0.14), residues: 3528 helix: 1.76 (0.16), residues: 1140 sheet: -0.15 (0.19), residues: 736 loop : -1.79 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 319 HIS 0.003 0.001 HIS E 160 PHE 0.023 0.001 PHE F 14 TYR 0.024 0.001 TYR M 392 ARG 0.008 0.000 ARG B 364 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 287 time to evaluate : 3.549 Fit side-chains REVERT: A 28 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7340 (mm) REVERT: A 133 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6831 (mm-30) REVERT: A 221 TYR cc_start: 0.5501 (p90) cc_final: 0.4731 (p90) REVERT: A 229 LYS cc_start: 0.6773 (ttpt) cc_final: 0.5861 (tmmt) REVERT: A 313 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7720 (tppt) REVERT: A 318 ASN cc_start: 0.8138 (m110) cc_final: 0.7758 (m-40) REVERT: A 391 PHE cc_start: 0.6433 (OUTLIER) cc_final: 0.4695 (t80) REVERT: B 1 MET cc_start: 0.8507 (tpt) cc_final: 0.8198 (tpt) REVERT: E 86 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7843 (tmmt) REVERT: E 122 MET cc_start: 0.6357 (mmt) cc_final: 0.6061 (mmt) REVERT: E 237 LYS cc_start: 0.6310 (mttt) cc_final: 0.6051 (ttmm) REVERT: E 244 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7411 (pp20) REVERT: E 257 ARG cc_start: 0.7046 (mmm-85) cc_final: 0.6828 (mmm-85) REVERT: E 260 GLU cc_start: 0.7285 (tp30) cc_final: 0.6889 (tp30) REVERT: E 393 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7523 (mt) REVERT: F 348 GLU cc_start: 0.6242 (pp20) cc_final: 0.5906 (pp20) REVERT: I 183 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7147 (mt-10) REVERT: I 193 MET cc_start: 0.4249 (tmt) cc_final: 0.3550 (tmm) REVERT: I 229 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7832 (pttp) REVERT: I 234 HIS cc_start: 0.5587 (t-90) cc_final: 0.5358 (t70) REVERT: I 284 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7566 (pt0) REVERT: M 45 PHE cc_start: 0.6099 (t80) cc_final: 0.5858 (t80) REVERT: M 261 CYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6997 (m) REVERT: M 307 LYS cc_start: 0.7538 (mptt) cc_final: 0.7129 (mppt) REVERT: N 1 MET cc_start: 0.8218 (tpp) cc_final: 0.7943 (mmm) REVERT: N 8 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: N 275 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7546 (ptt90) REVERT: N 348 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6563 (mt-10) REVERT: N 390 LYS cc_start: 0.8250 (tptm) cc_final: 0.8034 (tppp) REVERT: N 443 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8836 (mp) outliers start: 70 outliers final: 43 residues processed: 331 average time/residue: 1.5334 time to fit residues: 596.8726 Evaluate side-chains 337 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 281 time to evaluate : 3.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 273 ASP Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 449 GLU Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain N residue 275 ARG Chi-restraints excluded: chain N residue 276 ASN Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 443 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 4.9990 chunk 345 optimal weight: 0.9990 chunk 211 optimal weight: 0.6980 chunk 164 optimal weight: 0.5980 chunk 240 optimal weight: 0.7980 chunk 362 optimal weight: 3.9990 chunk 333 optimal weight: 3.9990 chunk 288 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 177 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33676 Z= 0.188 Angle : 0.558 16.227 46256 Z= 0.296 Chirality : 0.042 0.182 5076 Planarity : 0.004 0.047 5264 Dihedral : 18.235 179.765 6028 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.01 % Favored : 93.96 % Rotamer: Outliers : 2.14 % Allowed : 17.08 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.32 (0.14), residues: 3528 helix: 1.78 (0.16), residues: 1140 sheet: -0.11 (0.19), residues: 736 loop : -1.78 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 319 HIS 0.003 0.001 HIS E 160 PHE 0.015 0.001 PHE F 14 TYR 0.025 0.001 TYR M 392 ARG 0.008 0.000 ARG B 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 292 time to evaluate : 3.923 Fit side-chains REVERT: A 28 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7354 (mm) REVERT: A 133 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6827 (mm-30) REVERT: A 221 TYR cc_start: 0.5587 (p90) cc_final: 0.4727 (p90) REVERT: A 229 LYS cc_start: 0.6721 (ttpt) cc_final: 0.5795 (tmmt) REVERT: A 313 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7723 (tppt) REVERT: A 318 ASN cc_start: 0.8138 (m110) cc_final: 0.7756 (m-40) REVERT: A 391 PHE cc_start: 0.6396 (OUTLIER) cc_final: 0.4716 (t80) REVERT: B 1 MET cc_start: 0.8422 (tpt) cc_final: 0.7949 (tpp) REVERT: E 122 MET cc_start: 0.6402 (mmt) cc_final: 0.6096 (mmt) REVERT: E 237 LYS cc_start: 0.6293 (mttt) cc_final: 0.6044 (ttmm) REVERT: E 244 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7423 (pp20) REVERT: E 257 ARG cc_start: 0.7053 (mmm-85) cc_final: 0.6797 (mmm-85) REVERT: E 260 GLU cc_start: 0.7262 (tp30) cc_final: 0.6937 (tp30) REVERT: E 393 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7529 (mt) REVERT: F 278 VAL cc_start: 0.7735 (t) cc_final: 0.7532 (t) REVERT: F 348 GLU cc_start: 0.6263 (pp20) cc_final: 0.5921 (pp20) REVERT: I 122 MET cc_start: 0.7135 (ptm) cc_final: 0.6863 (ptm) REVERT: I 183 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: I 193 MET cc_start: 0.4169 (tmt) cc_final: 0.3486 (tmm) REVERT: I 229 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7801 (pttp) REVERT: I 234 HIS cc_start: 0.5576 (t-90) cc_final: 0.5312 (t70) REVERT: I 284 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: I 394 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7103 (mt-10) REVERT: M 45 PHE cc_start: 0.6076 (t80) cc_final: 0.5844 (t80) REVERT: M 261 CYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6996 (m) REVERT: M 307 LYS cc_start: 0.7562 (mptt) cc_final: 0.7199 (mppt) REVERT: N 1 MET cc_start: 0.8209 (tpp) cc_final: 0.7934 (mmm) REVERT: N 8 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: N 275 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7541 (ptt90) REVERT: N 348 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6589 (mt-10) REVERT: N 390 LYS cc_start: 0.8248 (tptm) cc_final: 0.8032 (tppp) REVERT: N 443 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8839 (mp) outliers start: 68 outliers final: 47 residues processed: 336 average time/residue: 1.6156 time to fit residues: 648.4227 Evaluate side-chains 342 residues out of total 3180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 281 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 449 GLU Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 253 SER Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 143 GLU Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain I residue 394 GLU Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 273 ASP Chi-restraints excluded: chain L residue 305 LEU Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 369 GLU Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 449 GLU Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain M residue 13 ASP Chi-restraints excluded: chain M residue 48 ASN Chi-restraints excluded: chain M residue 51 LYS Chi-restraints excluded: chain M residue 91 ASP Chi-restraints excluded: chain M residue 97 LEU Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 153 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 8 GLU Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain N residue 275 ARG Chi-restraints excluded: chain N residue 276 ASN Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 443 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 1.9990 chunk 307 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 121 optimal weight: 0.0470 chunk 296 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS A 370 ASN E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.133285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.111832 restraints weight = 53031.622| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.84 r_work: 0.3423 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33676 Z= 0.201 Angle : 0.566 16.286 46256 Z= 0.300 Chirality : 0.042 0.177 5076 Planarity : 0.004 0.048 5264 Dihedral : 18.234 179.443 6028 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.05 % Rotamer: Outliers : 2.17 % Allowed : 17.33 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.34 (0.14), residues: 3528 helix: 1.75 (0.16), residues: 1142 sheet: -0.11 (0.19), residues: 736 loop : -1.78 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 319 HIS 0.003 0.001 HIS E 160 PHE 0.015 0.002 PHE M 158 TYR 0.025 0.001 TYR M 392 ARG 0.008 0.000 ARG B 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10997.86 seconds wall clock time: 196 minutes 2.90 seconds (11762.90 seconds total)