Starting phenix.real_space_refine on Sat Jun 28 04:04:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ffi_29043/06_2025/8ffi_29043_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffi_29043/06_2025/8ffi_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/cci-nas-00/data/ceres_data/8ffi_29043/06_2025/8ffi_29043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffi_29043/06_2025/8ffi_29043.map" model { file = "/net/cci-nas-00/data/ceres_data/8ffi_29043/06_2025/8ffi_29043_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffi_29043/06_2025/8ffi_29043_neut.cif" } 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. Time to flip 19 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 20.50, per 1000 atoms: 0.63 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.37 Conformation dependent library (CDL) restraints added in 4.8 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: 19.89 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: 23.54 Time building geometry restraints manager: 10.07 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: 0.00 - 2.16: 45665 2.16 - 4.33: 551 4.33 - 6.49: 32 6.49 - 8.65: 3 8.65 - 10.82: 5 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 3.040 nonbonded pdb=" O GLY F 487 " pdb=" OG1 THR F 491 " model vdw 2.205 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 22.590 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: 0.040 Extract box with map and model: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 92.620 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.300 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:22.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.510 ------------------------------------------------------------------------------- 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= 0.125 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 Details of bonding type rmsd hydrogen bonds : bond 0.14455 ( 1235) hydrogen bonds : angle 6.23672 ( 3533) covalent geometry : bond 0.00258 (33676) covalent geometry : angle 0.56209 (46256) *********************** 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 to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 3.288 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: 1.5958 time to fit residues: 774.5406 Evaluate side-chains 301 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 3.433 ------------------------------------------------------------------------------- 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: 2.9990 chunk 186 optimal weight: 3.9990 chunk 147 optimal weight: 0.0770 chunk 285 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 chunk 330 optimal weight: 5.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 188 HIS 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.133367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.112000 restraints weight = 53138.777| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.77 r_work: 0.3437 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33676 Z= 0.138 Angle : 0.570 9.602 46256 Z= 0.306 Chirality : 0.043 0.272 5076 Planarity : 0.004 0.051 5264 Dihedral : 18.463 179.901 6030 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.12 % Favored : 93.85 % Rotamer: Outliers : 1.51 % Allowed : 8.21 % Favored : 90.28 % 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: -0.62 (0.14), residues: 3528 helix: 1.43 (0.16), residues: 1148 sheet: -0.35 (0.19), residues: 750 loop : -1.86 (0.14), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 33 HIS 0.005 0.001 HIS M 9 PHE 0.021 0.002 PHE F 14 TYR 0.017 0.001 TYR M 392 ARG 0.007 0.000 ARG L 243 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 1235) hydrogen bonds : angle 4.80948 ( 3533) covalent geometry : bond 0.00312 (33676) covalent geometry : angle 0.56986 (46256) *********************** 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 373 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 325 time to evaluate : 3.172 Fit side-chains REVERT: A 28 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7291 (mm) REVERT: A 133 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: A 161 ASP cc_start: 0.7642 (p0) cc_final: 0.7317 (p0) REVERT: A 229 LYS cc_start: 0.6839 (ttpt) cc_final: 0.5764 (tmmt) REVERT: B 8 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6863 (mm-30) REVERT: E 122 MET cc_start: 0.6855 (mmt) cc_final: 0.6518 (mmt) REVERT: E 189 GLU cc_start: 0.7280 (tt0) cc_final: 0.7040 (tt0) REVERT: E 260 GLU cc_start: 0.7343 (tp30) cc_final: 0.7134 (tp30) REVERT: E 299 LYS cc_start: 0.7311 (mtpt) cc_final: 0.7059 (ttpp) REVERT: F 314 LYS cc_start: 0.6795 (ptpp) cc_final: 0.6329 (mmtt) REVERT: F 356 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5817 (mt-10) REVERT: F 453 LYS cc_start: 0.8218 (ttmm) cc_final: 0.7974 (mtmt) REVERT: I 122 MET cc_start: 0.7373 (ptm) cc_final: 0.7111 (ptm) REVERT: I 284 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7672 (pt0) REVERT: L 1 MET cc_start: 0.7995 (tpt) cc_final: 0.7590 (tpt) REVERT: L 327 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8097 (tp-100) REVERT: L 350 ILE cc_start: 0.6910 (OUTLIER) cc_final: 0.6304 (mp) REVERT: M 307 LYS cc_start: 0.7526 (mptt) cc_final: 0.7037 (mtpt) REVERT: M 316 ASP cc_start: 0.7484 (p0) cc_final: 0.7078 (p0) REVERT: N 235 LYS cc_start: 0.8628 (mttm) cc_final: 0.8291 (mttt) REVERT: N 348 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6942 (mt-10) REVERT: N 415 GLU cc_start: 0.6869 (tp30) cc_final: 0.6624 (tp30) outliers start: 48 outliers final: 18 residues processed: 346 average time/residue: 1.6427 time to fit residues: 665.8184 Evaluate side-chains 317 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 291 time to evaluate : 3.205 ------------------------------------------------------------------------------- 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 246 ILE Chi-restraints excluded: chain B residue 8 GLU 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 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 I residue 66 SER Chi-restraints excluded: chain I residue 183 GLU Chi-restraints excluded: chain I residue 284 GLU Chi-restraints excluded: chain L residue 74 MET Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 327 GLN 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 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 96 optimal weight: 0.0020 chunk 124 optimal weight: 3.9990 chunk 342 optimal weight: 0.7980 chunk 24 optimal weight: 0.0370 chunk 310 optimal weight: 0.9980 chunk 252 optimal weight: 4.9990 chunk 247 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 361 optimal weight: 3.9990 chunk 172 optimal weight: 0.0980 overall best weight: 0.3866 ------------------------------------------------------------------------------- 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** ** F 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN N 276 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.135179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.113862 restraints weight = 53482.387| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.80 r_work: 0.3467 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1207 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= 0.112 Angle : 0.524 9.342 46256 Z= 0.282 Chirality : 0.041 0.204 5076 Planarity : 0.004 0.048 5264 Dihedral : 18.337 179.727 6028 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.93 % Favored : 95.04 % Rotamer: Outliers : 1.57 % Allowed : 10.50 % Favored : 87.92 % 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: 1.71 (0.16), residues: 1158 sheet: -0.18 (0.19), residues: 744 loop : -1.78 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 370 HIS 0.003 0.001 HIS E 160 PHE 0.014 0.001 PHE I 158 TYR 0.015 0.001 TYR A 221 ARG 0.008 0.000 ARG B 364 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 1235) hydrogen bonds : angle 4.49014 ( 3533) covalent geometry : bond 0.00246 (33676) covalent geometry : angle 0.52380 (46256) *********************** 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 363 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 313 time to evaluate : 3.686 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7258 (mm) REVERT: A 133 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: A 161 ASP cc_start: 0.7610 (p0) cc_final: 0.7295 (p0) REVERT: A 229 LYS cc_start: 0.6843 (ttpt) cc_final: 0.5777 (tmmt) REVERT: B 1 MET cc_start: 0.8454 (tpt) cc_final: 0.7770 (tpp) REVERT: B 85 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8358 (mtpt) REVERT: E 89 LYS cc_start: 0.7115 (mmtm) cc_final: 0.6876 (mmtm) REVERT: E 122 MET cc_start: 0.6739 (mmt) cc_final: 0.6414 (mmt) REVERT: E 189 GLU cc_start: 0.7305 (tt0) cc_final: 0.7104 (tt0) REVERT: E 244 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7514 (pp20) REVERT: E 260 GLU cc_start: 0.7323 (tp30) cc_final: 0.7087 (tp30) REVERT: F 314 LYS cc_start: 0.6658 (ptpp) cc_final: 0.6379 (mmtt) REVERT: F 373 PHE cc_start: 0.7943 (m-10) cc_final: 0.7603 (m-10) REVERT: I 234 HIS cc_start: 0.5841 (t-90) cc_final: 0.5470 (t70) REVERT: I 284 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7682 (pt0) REVERT: L 1 MET cc_start: 0.8049 (tpt) cc_final: 0.7578 (tpt) REVERT: L 327 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7987 (tp-100) REVERT: M 261 CYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7211 (m) REVERT: M 307 LYS cc_start: 0.7581 (mptt) cc_final: 0.7088 (mppt) REVERT: N 235 LYS cc_start: 0.8612 (mttm) cc_final: 0.8286 (mttt) REVERT: N 348 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6937 (mt-10) REVERT: N 430 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7617 (mp-120) outliers start: 50 outliers final: 21 residues processed: 335 average time/residue: 1.5377 time to fit residues: 604.7974 Evaluate side-chains 312 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 282 time to evaluate : 3.398 ------------------------------------------------------------------------------- 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 B residue 85 LYS 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 F residue 331 GLU Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain I residue 66 SER 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 74 MET Chi-restraints excluded: chain L residue 327 GLN Chi-restraints excluded: chain L residue 344 GLN Chi-restraints excluded: chain L residue 496 ILE 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 276 ASN 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 264 optimal weight: 2.9990 chunk 347 optimal weight: 0.7980 chunk 266 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 323 optimal weight: 0.6980 chunk 309 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 F 129 ASN M 370 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.131189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.109317 restraints weight = 52873.255| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.75 r_work: 0.3387 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33676 Z= 0.201 Angle : 0.634 10.740 46256 Z= 0.337 Chirality : 0.045 0.195 5076 Planarity : 0.005 0.054 5264 Dihedral : 18.466 179.417 6028 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.69 % Favored : 93.28 % Rotamer: Outliers : 2.36 % Allowed : 11.57 % Favored : 86.07 % 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: -0.63 (0.14), residues: 3528 helix: 1.41 (0.16), residues: 1154 sheet: -0.32 (0.19), residues: 742 loop : -1.88 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 319 HIS 0.005 0.001 HIS B 59 PHE 0.019 0.002 PHE I 45 TYR 0.023 0.002 TYR M 392 ARG 0.006 0.001 ARG E 257 Details of bonding type rmsd hydrogen bonds : bond 0.05039 ( 1235) hydrogen bonds : angle 4.75967 ( 3533) covalent geometry : bond 0.00476 (33676) covalent geometry : angle 0.63435 (46256) *********************** 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 373 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 298 time to evaluate : 3.392 Fit side-chains REVERT: A 28 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7292 (mm) REVERT: A 133 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: A 189 GLU cc_start: 0.8301 (tt0) cc_final: 0.8096 (tt0) REVERT: A 190 TYR cc_start: 0.7560 (m-10) cc_final: 0.7244 (m-10) REVERT: A 221 TYR cc_start: 0.5699 (p90) cc_final: 0.4800 (p90) REVERT: A 229 LYS cc_start: 0.6895 (ttpt) cc_final: 0.5815 (tmmt) REVERT: A 391 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.4868 (t80) REVERT: B 8 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6905 (mm-30) REVERT: B 85 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8451 (mtpt) REVERT: B 364 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8475 (mtt-85) REVERT: E 89 LYS cc_start: 0.7159 (mmtm) cc_final: 0.6914 (mmtm) REVERT: E 122 MET cc_start: 0.6949 (mmt) cc_final: 0.6733 (mpp) REVERT: E 189 GLU cc_start: 0.7381 (tt0) cc_final: 0.7135 (tt0) REVERT: E 244 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7591 (pp20) REVERT: E 260 GLU cc_start: 0.7504 (tp30) cc_final: 0.7256 (tp30) REVERT: E 283 GLN cc_start: 0.7029 (mm-40) cc_final: 0.6586 (mm-40) REVERT: E 393 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7522 (mt) REVERT: F 356 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5793 (mt-10) REVERT: I 234 HIS cc_start: 0.5939 (t-90) cc_final: 0.5579 (t70) REVERT: I 277 MET cc_start: 0.7510 (mmm) cc_final: 0.7309 (mmt) REVERT: I 284 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7687 (pt0) REVERT: L 435 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7268 (mtt) REVERT: M 307 LYS cc_start: 0.7770 (mptt) cc_final: 0.7264 (mppt) REVERT: N 235 LYS cc_start: 0.8657 (mttm) cc_final: 0.8320 (mttt) REVERT: N 348 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6977 (mt-10) REVERT: N 430 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7780 (mp-120) outliers start: 75 outliers final: 32 residues processed: 337 average time/residue: 1.6668 time to fit residues: 675.2439 Evaluate side-chains 332 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 287 time to evaluate : 3.818 ------------------------------------------------------------------------------- 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 133 GLU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 203 LEU 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 364 ARG 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 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 334 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 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 161 ASP 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 317 VAL Chi-restraints excluded: chain L residue 327 GLN Chi-restraints excluded: chain L residue 344 GLN 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 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 203 ASP Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 430 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 342 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 351 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 360 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 66 optimal weight: 0.0060 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 ASN M 370 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.131256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.109448 restraints weight = 52776.586| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.75 r_work: 0.3390 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33676 Z= 0.186 Angle : 0.618 11.137 46256 Z= 0.329 Chirality : 0.045 0.230 5076 Planarity : 0.005 0.055 5264 Dihedral : 18.436 179.783 6028 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.55 % Allowed : 13.14 % Favored : 84.31 % 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: 1.34 (0.16), residues: 1140 sheet: -0.32 (0.19), residues: 738 loop : -1.93 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 319 HIS 0.004 0.001 HIS A 160 PHE 0.017 0.002 PHE I 45 TYR 0.023 0.002 TYR M 392 ARG 0.005 0.000 ARG M 374 Details of bonding type rmsd hydrogen bonds : bond 0.04797 ( 1235) hydrogen bonds : angle 4.72549 ( 3533) covalent geometry : bond 0.00438 (33676) covalent geometry : angle 0.61806 (46256) *********************** 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 371 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 290 time to evaluate : 3.945 Fit side-chains REVERT: A 28 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7289 (mm) REVERT: A 133 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: A 189 GLU cc_start: 0.8250 (tt0) cc_final: 0.8044 (tt0) REVERT: A 190 TYR cc_start: 0.7614 (m-10) cc_final: 0.7322 (m-10) REVERT: A 221 TYR cc_start: 0.5623 (p90) cc_final: 0.4862 (p90) REVERT: A 229 LYS cc_start: 0.6999 (ttpt) cc_final: 0.5827 (pptt) REVERT: A 391 PHE cc_start: 0.6883 (OUTLIER) cc_final: 0.4890 (t80) REVERT: A 399 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7755 (mm-30) REVERT: B 1 MET cc_start: 0.8532 (tpt) cc_final: 0.7920 (tpt) REVERT: B 8 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6894 (mm-30) REVERT: B 85 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8434 (mtpt) REVERT: B 364 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8484 (mtt-85) REVERT: E 86 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7872 (tmmt) REVERT: E 89 LYS cc_start: 0.7220 (mmtm) cc_final: 0.6958 (mmtm) REVERT: E 122 MET cc_start: 0.6939 (mmt) cc_final: 0.6698 (mpp) REVERT: E 189 GLU cc_start: 0.7429 (tt0) cc_final: 0.7141 (tt0) REVERT: E 244 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7589 (pp20) REVERT: E 260 GLU cc_start: 0.7494 (tp30) cc_final: 0.7241 (tp30) REVERT: E 393 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7547 (mt) REVERT: F 348 GLU cc_start: 0.6268 (pp20) cc_final: 0.5937 (pp20) REVERT: F 356 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5792 (mt-10) REVERT: F 453 LYS cc_start: 0.8284 (ttmm) cc_final: 0.8016 (mtmt) REVERT: I 229 LYS cc_start: 0.8022 (mtmt) cc_final: 0.7184 (pttp) REVERT: I 234 HIS cc_start: 0.5926 (t-90) cc_final: 0.5575 (t70) REVERT: I 277 MET cc_start: 0.7517 (mmm) cc_final: 0.7294 (mmt) REVERT: I 394 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: L 350 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6342 (mp) REVERT: L 435 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7290 (mtt) REVERT: M 45 PHE cc_start: 0.6209 (t80) cc_final: 0.5798 (t80) REVERT: N 235 LYS cc_start: 0.8638 (mttm) cc_final: 0.8308 (mttt) REVERT: N 243 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7560 (mtt180) REVERT: N 275 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7433 (ptt90) REVERT: N 348 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: N 430 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7783 (mp-120) outliers start: 81 outliers final: 39 residues processed: 333 average time/residue: 1.8541 time to fit residues: 725.0821 Evaluate side-chains 337 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 3.460 ------------------------------------------------------------------------------- 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 133 GLU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 85 LYS 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 364 ARG 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 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 356 GLU Chi-restraints excluded: chain F residue 400 GLU 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 143 GLU Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 ASP 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 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 391 THR Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain L residue 498 THR 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 203 ASP Chi-restraints excluded: chain N residue 243 ARG Chi-restraints excluded: chain N residue 275 ARG Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 430 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 328 optimal weight: 0.5980 chunk 355 optimal weight: 1.9990 chunk 277 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 275 optimal weight: 1.9990 chunk 313 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 370 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.130758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.108890 restraints weight = 52796.608| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.75 r_work: 0.3380 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33676 Z= 0.199 Angle : 0.637 11.984 46256 Z= 0.339 Chirality : 0.046 0.216 5076 Planarity : 0.005 0.058 5264 Dihedral : 18.460 179.759 6028 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.64 % Allowed : 14.09 % Favored : 83.27 % 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: -0.80 (0.14), residues: 3528 helix: 1.27 (0.16), residues: 1140 sheet: -0.37 (0.19), residues: 738 loop : -1.96 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 319 HIS 0.004 0.001 HIS E 160 PHE 0.018 0.002 PHE I 45 TYR 0.023 0.002 TYR M 392 ARG 0.005 0.001 ARG M 374 Details of bonding type rmsd hydrogen bonds : bond 0.04994 ( 1235) hydrogen bonds : angle 4.76220 ( 3533) covalent geometry : bond 0.00469 (33676) covalent geometry : angle 0.63705 (46256) *********************** 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 380 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 296 time to evaluate : 4.423 Fit side-chains REVERT: A 28 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7320 (mm) REVERT: A 133 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: A 189 GLU cc_start: 0.8266 (tt0) cc_final: 0.8052 (tt0) REVERT: A 190 TYR cc_start: 0.7646 (m-10) cc_final: 0.7336 (m-10) REVERT: A 221 TYR cc_start: 0.5696 (p90) cc_final: 0.4898 (p90) REVERT: A 222 ASP cc_start: 0.5313 (m-30) cc_final: 0.5107 (m-30) REVERT: A 229 LYS cc_start: 0.6961 (ttpt) cc_final: 0.5779 (pptt) REVERT: A 391 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.4936 (t80) REVERT: A 399 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: B 1 MET cc_start: 0.8514 (tpt) cc_final: 0.7848 (tpt) REVERT: B 8 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6922 (mm-30) REVERT: B 85 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8468 (mtpt) REVERT: B 364 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8499 (mtt-85) REVERT: E 122 MET cc_start: 0.6972 (mmt) cc_final: 0.6762 (mpp) REVERT: E 189 GLU cc_start: 0.7428 (tt0) cc_final: 0.7097 (tt0) REVERT: E 244 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7595 (pp20) REVERT: E 260 GLU cc_start: 0.7521 (tp30) cc_final: 0.7206 (tp30) REVERT: E 393 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7659 (mt) REVERT: I 193 MET cc_start: 0.4650 (tmt) cc_final: 0.3985 (tmm) REVERT: I 229 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7383 (pttp) REVERT: I 234 HIS cc_start: 0.5944 (t-90) cc_final: 0.5583 (t70) REVERT: I 277 MET cc_start: 0.7557 (mmm) cc_final: 0.7327 (mmt) REVERT: I 394 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7367 (mt-10) REVERT: L 350 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6383 (mp) REVERT: L 435 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7291 (mtt) REVERT: M 307 LYS cc_start: 0.7703 (mptt) cc_final: 0.7246 (mppt) REVERT: M 370 ASN cc_start: 0.7400 (t0) cc_final: 0.7184 (t0) REVERT: N 235 LYS cc_start: 0.8650 (mttm) cc_final: 0.8315 (mttt) REVERT: N 243 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7579 (mtt180) REVERT: N 275 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7459 (ptt90) REVERT: N 348 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7098 (mt-10) REVERT: N 430 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7784 (mp-120) outliers start: 84 outliers final: 42 residues processed: 345 average time/residue: 2.0313 time to fit residues: 838.5144 Evaluate side-chains 346 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 288 time to evaluate : 3.883 ------------------------------------------------------------------------------- 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 133 GLU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 85 LYS 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 364 ARG 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 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 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 143 GLU Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 161 ASP Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 309 MET 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 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 391 THR Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain L residue 498 THR 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 153 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 243 ARG Chi-restraints excluded: chain N residue 275 ARG Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 430 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 134 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 207 optimal weight: 0.1980 chunk 340 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 290 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** M 3 ASN M 318 ASN N 18 GLN N 276 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.131437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.109567 restraints weight = 53026.484| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.76 r_work: 0.3393 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33676 Z= 0.171 Angle : 0.609 13.645 46256 Z= 0.325 Chirality : 0.044 0.240 5076 Planarity : 0.005 0.055 5264 Dihedral : 18.410 179.102 6028 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.58 % Allowed : 14.72 % Favored : 82.70 % 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: -0.71 (0.14), residues: 3528 helix: 1.38 (0.16), residues: 1140 sheet: -0.33 (0.19), residues: 736 loop : -1.94 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 319 HIS 0.004 0.001 HIS E 160 PHE 0.015 0.002 PHE I 45 TYR 0.014 0.001 TYR A 221 ARG 0.007 0.000 ARG M 19 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 1235) hydrogen bonds : angle 4.67650 ( 3533) covalent geometry : bond 0.00400 (33676) covalent geometry : angle 0.60896 (46256) *********************** 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 374 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 292 time to evaluate : 3.330 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7296 (mm) REVERT: A 133 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: A 190 TYR cc_start: 0.7652 (m-10) cc_final: 0.7352 (m-10) REVERT: A 221 TYR cc_start: 0.5691 (p90) cc_final: 0.4918 (p90) REVERT: A 386 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6782 (m-30) REVERT: A 391 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.5004 (t80) REVERT: A 399 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7703 (mm-30) REVERT: B 8 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6872 (mm-30) REVERT: B 85 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8439 (mtpt) REVERT: B 364 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8485 (mtt-85) REVERT: E 86 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7861 (tmmt) REVERT: E 122 MET cc_start: 0.6934 (mmt) cc_final: 0.6728 (mpp) REVERT: E 189 GLU cc_start: 0.7422 (tt0) cc_final: 0.7073 (tt0) REVERT: E 244 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7594 (pp20) REVERT: E 260 GLU cc_start: 0.7497 (tp30) cc_final: 0.7248 (tp30) REVERT: E 393 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7662 (mt) REVERT: F 348 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5979 (pp20) REVERT: I 193 MET cc_start: 0.4661 (tmt) cc_final: 0.4401 (tmm) REVERT: L 350 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6318 (mp) REVERT: L 435 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7269 (mtt) REVERT: M 45 PHE cc_start: 0.6316 (t80) cc_final: 0.6028 (t80) REVERT: M 307 LYS cc_start: 0.7675 (mptt) cc_final: 0.7186 (mppt) REVERT: N 235 LYS cc_start: 0.8650 (mttm) cc_final: 0.8310 (mttt) REVERT: N 243 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.8028 (mtp85) REVERT: N 275 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7454 (ptt90) REVERT: N 348 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: N 430 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7770 (mp-120) outliers start: 82 outliers final: 42 residues processed: 343 average time/residue: 1.6359 time to fit residues: 662.7031 Evaluate side-chains 346 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 287 time to evaluate : 3.688 ------------------------------------------------------------------------------- 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 203 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 364 ARG 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 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 400 GLU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 204 THR 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 305 LEU 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 391 THR Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 449 GLU Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain L residue 498 THR 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 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 57 LEU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 243 ARG Chi-restraints excluded: chain N residue 275 ARG Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 430 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 97 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 307 optimal weight: 0.8980 chunk 269 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 315 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 M 318 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 = 0.3838 r_free = 0.3838 target = 0.129501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.108204 restraints weight = 52867.919| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.79 r_work: 0.3367 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1617 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= 0.257 Angle : 0.707 12.524 46256 Z= 0.374 Chirality : 0.048 0.222 5076 Planarity : 0.005 0.063 5264 Dihedral : 18.511 179.072 6028 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 2.89 % Allowed : 15.09 % Favored : 82.01 % 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: -0.98 (0.14), residues: 3528 helix: 1.04 (0.15), residues: 1146 sheet: -0.44 (0.19), residues: 746 loop : -2.05 (0.14), residues: 1636 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 0.008 0.001 ARG E 257 Details of bonding type rmsd hydrogen bonds : bond 0.05654 ( 1235) hydrogen bonds : angle 4.91473 ( 3533) covalent geometry : bond 0.00613 (33676) covalent geometry : angle 0.70693 (46256) *********************** 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 389 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 297 time to evaluate : 3.170 Fit side-chains REVERT: A 19 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6722 (ttt180) REVERT: A 28 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7250 (mm) REVERT: A 133 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: A 189 GLU cc_start: 0.8209 (tt0) cc_final: 0.7995 (tt0) REVERT: A 190 TYR cc_start: 0.7667 (m-10) cc_final: 0.7337 (m-10) REVERT: A 221 TYR cc_start: 0.5854 (p90) cc_final: 0.5067 (p90) REVERT: A 297 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7195 (ttpp) REVERT: A 391 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.5423 (t80) REVERT: A 399 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: B 8 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6856 (mm-30) REVERT: B 85 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8493 (mtpt) REVERT: B 364 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8476 (mtt-85) REVERT: E 86 LYS cc_start: 0.8160 (ttmm) cc_final: 0.7826 (tmmt) REVERT: E 122 MET cc_start: 0.6917 (mmt) cc_final: 0.6704 (mpp) REVERT: E 189 GLU cc_start: 0.7421 (tt0) cc_final: 0.7083 (tt0) REVERT: E 223 PHE cc_start: 0.6061 (OUTLIER) cc_final: 0.4637 (p90) REVERT: E 244 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7526 (pp20) REVERT: E 257 ARG cc_start: 0.7348 (mmm-85) cc_final: 0.7046 (mmm160) REVERT: E 260 GLU cc_start: 0.7546 (tp30) cc_final: 0.7301 (tp30) REVERT: E 393 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7710 (mt) REVERT: F 348 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.6065 (pp20) REVERT: I 143 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7192 (tp30) REVERT: I 223 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.5623 (p90) REVERT: L 350 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6429 (mp) REVERT: L 435 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7294 (mtt) REVERT: M 45 PHE cc_start: 0.6410 (t80) cc_final: 0.6113 (t80) REVERT: M 307 LYS cc_start: 0.7691 (mptt) cc_final: 0.7166 (mppt) REVERT: M 370 ASN cc_start: 0.7393 (t0) cc_final: 0.7181 (t0) REVERT: N 235 LYS cc_start: 0.8645 (mttm) cc_final: 0.8272 (mttt) REVERT: N 275 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7436 (ptt90) REVERT: N 348 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: N 430 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7833 (mp-120) REVERT: N 443 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8763 (mp) outliers start: 92 outliers final: 51 residues processed: 355 average time/residue: 1.5410 time to fit residues: 642.1123 Evaluate side-chains 359 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 287 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 19 ARG 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 203 LEU Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 297 LYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 85 LYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 364 ARG 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 155 GLN Chi-restraints excluded: chain E residue 223 PHE 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 74 MET Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 348 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 143 GLU Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 223 PHE 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 305 LEU 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 369 GLU Chi-restraints excluded: chain L residue 391 THR Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 449 GLU Chi-restraints excluded: chain L residue 496 ILE Chi-restraints excluded: chain L residue 498 THR 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 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 57 LEU Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 275 ARG Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 430 GLN Chi-restraints excluded: chain N residue 443 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 69 optimal weight: 0.5980 chunk 304 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 257 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 chunk 279 optimal weight: 4.9990 chunk 233 optimal weight: 0.0980 chunk 165 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 246 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** F 409 ASN M 3 ASN N 18 GLN N 131 ASN N 276 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.132679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.110951 restraints weight = 53106.230| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.76 r_work: 0.3414 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1490 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= 0.135 Angle : 0.584 15.091 46256 Z= 0.313 Chirality : 0.043 0.336 5076 Planarity : 0.004 0.053 5264 Dihedral : 18.353 179.187 6028 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.33 % Allowed : 16.04 % Favored : 81.64 % 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: -0.62 (0.14), residues: 3528 helix: 1.52 (0.16), residues: 1144 sheet: -0.31 (0.19), residues: 736 loop : -1.92 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 319 HIS 0.004 0.001 HIS E 160 PHE 0.026 0.002 PHE F 14 TYR 0.017 0.001 TYR M 225 ARG 0.007 0.000 ARG E 257 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 1235) hydrogen bonds : angle 4.56239 ( 3533) covalent geometry : bond 0.00305 (33676) covalent geometry : angle 0.58390 (46256) *********************** 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 360 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 286 time to evaluate : 3.455 Fit side-chains REVERT: A 19 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6798 (ttt180) REVERT: A 28 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7303 (mm) REVERT: A 129 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7240 (mttp) REVERT: A 133 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: A 190 TYR cc_start: 0.7595 (m-10) cc_final: 0.7305 (m-10) REVERT: A 193 MET cc_start: 0.2820 (mmt) cc_final: 0.1859 (ttm) REVERT: A 221 TYR cc_start: 0.5747 (p90) cc_final: 0.4941 (p90) REVERT: A 313 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7825 (tppt) REVERT: A 318 ASN cc_start: 0.8183 (m110) cc_final: 0.7718 (m-40) REVERT: A 391 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.4931 (t80) REVERT: B 1 MET cc_start: 0.8573 (tpt) cc_final: 0.7857 (tpp) REVERT: B 8 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6809 (mm-30) REVERT: B 85 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8399 (mtpt) REVERT: B 364 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8460 (mtt-85) REVERT: E 86 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7865 (tmmt) REVERT: E 189 GLU cc_start: 0.7390 (tt0) cc_final: 0.7041 (tt0) REVERT: E 244 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7549 (pp20) REVERT: E 257 ARG cc_start: 0.7274 (mmm-85) cc_final: 0.6982 (mmm160) REVERT: E 260 GLU cc_start: 0.7476 (tp30) cc_final: 0.7104 (tp30) REVERT: F 348 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.5930 (pp20) REVERT: I 122 MET cc_start: 0.7436 (ptm) cc_final: 0.7157 (ptm) REVERT: L 350 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6187 (mp) REVERT: M 45 PHE cc_start: 0.6281 (t80) cc_final: 0.5858 (t80) REVERT: M 261 CYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7238 (m) REVERT: M 307 LYS cc_start: 0.7727 (mptt) cc_final: 0.7199 (mppt) REVERT: N 235 LYS cc_start: 0.8616 (mttm) cc_final: 0.8290 (mttt) REVERT: N 275 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7455 (ptt90) REVERT: N 348 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7019 (mt-10) REVERT: N 430 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7756 (mp-120) outliers start: 74 outliers final: 37 residues processed: 332 average time/residue: 1.5397 time to fit residues: 600.8448 Evaluate side-chains 331 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 278 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 ASN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 203 LEU 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 85 LYS Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 364 ARG 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 F residue 331 GLU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 400 GLU 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 157 ILE Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 305 LEU 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 369 GLU Chi-restraints excluded: chain L residue 496 ILE 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 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 12 ILE Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain N residue 203 ASP Chi-restraints excluded: chain N residue 275 ARG Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 430 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 162 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 233 optimal weight: 0.2980 chunk 209 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 353 optimal weight: 1.9990 chunk 334 optimal weight: 3.9990 chunk 218 optimal weight: 0.7980 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 E 320 HIS E 364 GLN ** E 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN M 102 GLN 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 = 0.3876 r_free = 0.3876 target = 0.132088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110808 restraints weight = 52907.136| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.82 r_work: 0.3407 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33676 Z= 0.152 Angle : 0.604 15.486 46256 Z= 0.322 Chirality : 0.044 0.309 5076 Planarity : 0.005 0.053 5264 Dihedral : 18.324 179.274 6028 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.63 % Favored : 93.34 % Rotamer: Outliers : 1.92 % Allowed : 16.26 % Favored : 81.82 % 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: -0.61 (0.14), residues: 3528 helix: 1.53 (0.16), residues: 1140 sheet: -0.41 (0.19), residues: 760 loop : -1.87 (0.14), residues: 1628 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 0.028 0.002 PHE F 14 TYR 0.024 0.001 TYR M 392 ARG 0.007 0.000 ARG E 257 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 1235) hydrogen bonds : angle 4.58156 ( 3533) covalent geometry : bond 0.00352 (33676) covalent geometry : angle 0.60434 (46256) ********************** 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 353 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 292 time to evaluate : 3.232 Fit side-chains REVERT: A 28 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7275 (mm) REVERT: A 129 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7192 (mttp) REVERT: A 133 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: A 190 TYR cc_start: 0.7619 (m-10) cc_final: 0.7338 (m-10) REVERT: A 221 TYR cc_start: 0.5747 (p90) cc_final: 0.4952 (p90) REVERT: A 313 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7798 (tppt) REVERT: A 318 ASN cc_start: 0.8155 (m110) cc_final: 0.7694 (m-40) REVERT: A 391 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.4748 (t80) REVERT: B 8 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6797 (mm-30) REVERT: B 85 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8413 (mtpt) REVERT: B 364 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8492 (mtt-85) REVERT: E 189 GLU cc_start: 0.7377 (tt0) cc_final: 0.7017 (tt0) REVERT: E 244 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7529 (pp20) REVERT: E 257 ARG cc_start: 0.7276 (mmm-85) cc_final: 0.6974 (mmm160) REVERT: E 260 GLU cc_start: 0.7452 (tp30) cc_final: 0.7082 (tp30) REVERT: F 348 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5950 (pp20) REVERT: I 122 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7160 (ptm) REVERT: I 193 MET cc_start: 0.4345 (tmt) cc_final: 0.4109 (tmm) REVERT: I 229 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7292 (pttp) REVERT: I 234 HIS cc_start: 0.5856 (t-90) cc_final: 0.5570 (t70) REVERT: L 283 LEU cc_start: 0.8253 (mt) cc_final: 0.8048 (tp) REVERT: L 350 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6218 (mp) REVERT: M 45 PHE cc_start: 0.6236 (t80) cc_final: 0.5817 (t80) REVERT: M 307 LYS cc_start: 0.7720 (mptt) cc_final: 0.7218 (mppt) REVERT: N 235 LYS cc_start: 0.8631 (mttm) cc_final: 0.8287 (mttt) REVERT: N 275 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7448 (ptt90) REVERT: N 348 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7039 (mt-10) REVERT: N 430 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7746 (mp-120) outliers start: 61 outliers final: 39 residues processed: 330 average time/residue: 1.5031 time to fit residues: 584.7988 Evaluate side-chains 338 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 284 time to evaluate : 3.419 ------------------------------------------------------------------------------- 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 129 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 203 LEU 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 85 LYS 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 364 ARG 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 F residue 298 CYS Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 400 GLU 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 157 ILE Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 316 ASP Chi-restraints excluded: chain L residue 89 THR Chi-restraints excluded: chain L residue 305 LEU 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 369 GLU Chi-restraints excluded: chain L residue 496 ILE 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 153 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 261 CYS 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 275 ARG Chi-restraints excluded: chain N residue 348 GLU Chi-restraints excluded: chain N residue 430 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 355 optimal weight: 0.5980 chunk 268 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 263 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 341 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 308 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 M 102 GLN N 18 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.132247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.110364 restraints weight = 52731.792| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.73 r_work: 0.3406 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33676 Z= 0.153 Angle : 0.603 16.605 46256 Z= 0.320 Chirality : 0.044 0.304 5076 Planarity : 0.005 0.052 5264 Dihedral : 18.317 179.149 6028 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.93 % Rotamer: Outliers : 2.17 % Allowed : 16.29 % Favored : 81.54 % 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: -0.57 (0.14), residues: 3528 helix: 1.55 (0.16), residues: 1140 sheet: -0.38 (0.19), residues: 758 loop : -1.85 (0.14), residues: 1630 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 0.025 0.002 PHE F 14 TYR 0.025 0.001 TYR M 392 ARG 0.007 0.000 ARG E 257 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 1235) hydrogen bonds : angle 4.57294 ( 3533) covalent geometry : bond 0.00353 (33676) covalent geometry : angle 0.60309 (46256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26758.02 seconds wall clock time: 462 minutes 53.47 seconds (27773.47 seconds total)