Starting phenix.real_space_refine (version: 1.19rc7) on Thu Jan 7 17:23:04 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1r_9318/01_2021/6n1r_9318_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1r_9318/01_2021/6n1r_9318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1r_9318/01_2021/6n1r_9318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1r_9318/01_2021/6n1r_9318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1r_9318/01_2021/6n1r_9318_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1r_9318/01_2021/6n1r_9318_neut.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 46044 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3837 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain: "B" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3837 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain: "C" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3837 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain: "D" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3837 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain: "E" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3837 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain: "F" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3837 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain: "G" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3837 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain: "H" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3837 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain: "I" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3837 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain: "J" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3837 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain: "K" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3837 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 17, 'TRANS': 465} Chain: "L" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3837 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 17, 'TRANS': 465} Time building chain proxies: 23.31, per 1000 atoms: 0.51 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Number of scatterers: 46044 At special positions: 0 Unit cell: (186.16, 189.28, 159.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 252 16.00 O 8604 8.00 N 8292 7.00 C 28896 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.65 Conformation dependent library (CDL) restraints added in 7.7 seconds 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10944 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 60 sheets defined 54.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 12 through 30 Processing helix chain 'A' and resid 40 through 53 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 198 Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 386 Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.720A pdb=" N VAL A 390 " --> pdb=" O HIS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 30 Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 64 through 75 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 198 Processing helix chain 'B' and resid 202 through 208 Processing helix chain 'B' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 280 Processing helix chain 'B' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE B 313 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 386 Processing helix chain 'B' and resid 386 through 396 removed outlier: 3.721A pdb=" N VAL B 390 " --> pdb=" O HIS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 414 through 423 Processing helix chain 'B' and resid 425 through 429 Processing helix chain 'B' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 30 Processing helix chain 'C' and resid 40 through 53 Processing helix chain 'C' and resid 64 through 75 Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 162 through 168 removed outlier: 3.669A pdb=" N VAL C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 198 Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'C' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 Processing helix chain 'C' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE C 313 " --> pdb=" O SER C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 386 Processing helix chain 'C' and resid 386 through 396 removed outlier: 3.721A pdb=" N VAL C 390 " --> pdb=" O HIS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 412 Processing helix chain 'C' and resid 414 through 423 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 30 Processing helix chain 'D' and resid 40 through 53 Processing helix chain 'D' and resid 64 through 75 Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL D 166 " --> pdb=" O PRO D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 198 Processing helix chain 'D' and resid 202 through 208 Processing helix chain 'D' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 280 Processing helix chain 'D' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 386 Processing helix chain 'D' and resid 386 through 396 removed outlier: 3.720A pdb=" N VAL D 390 " --> pdb=" O HIS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 414 through 423 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 30 Processing helix chain 'E' and resid 40 through 53 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 128 through 133 Processing helix chain 'E' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 198 Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 223 through 234 removed outlier: 3.733A pdb=" N ILE E 227 " --> pdb=" O GLY E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 280 Processing helix chain 'E' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 386 Processing helix chain 'E' and resid 386 through 396 removed outlier: 3.721A pdb=" N VAL E 390 " --> pdb=" O HIS E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 412 Processing helix chain 'E' and resid 414 through 423 Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS E 436 " --> pdb=" O LEU E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 477 removed outlier: 3.704A pdb=" N VAL E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 30 Processing helix chain 'F' and resid 40 through 53 Processing helix chain 'F' and resid 64 through 75 Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 128 through 133 Processing helix chain 'F' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL F 166 " --> pdb=" O PRO F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 198 Processing helix chain 'F' and resid 202 through 208 Processing helix chain 'F' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 280 Processing helix chain 'F' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE F 313 " --> pdb=" O SER F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 386 Processing helix chain 'F' and resid 386 through 396 removed outlier: 3.721A pdb=" N VAL F 390 " --> pdb=" O HIS F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 412 Processing helix chain 'F' and resid 414 through 423 Processing helix chain 'F' and resid 425 through 429 Processing helix chain 'F' and resid 430 through 457 removed outlier: 4.202A pdb=" N LYS F 436 " --> pdb=" O LEU F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL F 461 " --> pdb=" O LYS F 457 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 30 Processing helix chain 'G' and resid 40 through 53 Processing helix chain 'G' and resid 64 through 75 Processing helix chain 'G' and resid 79 through 91 Processing helix chain 'G' and resid 128 through 133 Processing helix chain 'G' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL G 166 " --> pdb=" O PRO G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 198 Processing helix chain 'G' and resid 202 through 208 Processing helix chain 'G' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE G 227 " --> pdb=" O GLY G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 280 Processing helix chain 'G' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE G 313 " --> pdb=" O SER G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 386 Processing helix chain 'G' and resid 386 through 396 removed outlier: 3.721A pdb=" N VAL G 390 " --> pdb=" O HIS G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 399 through 412 Processing helix chain 'G' and resid 414 through 423 Processing helix chain 'G' and resid 425 through 429 Processing helix chain 'G' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS G 436 " --> pdb=" O LEU G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 477 removed outlier: 3.706A pdb=" N VAL G 461 " --> pdb=" O LYS G 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 30 Processing helix chain 'H' and resid 40 through 53 Processing helix chain 'H' and resid 64 through 75 Processing helix chain 'H' and resid 79 through 91 Processing helix chain 'H' and resid 128 through 133 Processing helix chain 'H' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL H 166 " --> pdb=" O PRO H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 198 Processing helix chain 'H' and resid 202 through 208 Processing helix chain 'H' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE H 227 " --> pdb=" O GLY H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 280 Processing helix chain 'H' and resid 309 through 321 removed outlier: 3.731A pdb=" N ILE H 313 " --> pdb=" O SER H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 343 through 386 Processing helix chain 'H' and resid 386 through 396 removed outlier: 3.720A pdb=" N VAL H 390 " --> pdb=" O HIS H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 399 through 412 Processing helix chain 'H' and resid 414 through 423 Processing helix chain 'H' and resid 425 through 429 Processing helix chain 'H' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS H 436 " --> pdb=" O LEU H 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL H 461 " --> pdb=" O LYS H 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 30 Processing helix chain 'I' and resid 40 through 53 Processing helix chain 'I' and resid 64 through 75 Processing helix chain 'I' and resid 79 through 91 Processing helix chain 'I' and resid 128 through 133 Processing helix chain 'I' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL I 166 " --> pdb=" O PRO I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 198 Processing helix chain 'I' and resid 202 through 208 Processing helix chain 'I' and resid 223 through 234 removed outlier: 3.733A pdb=" N ILE I 227 " --> pdb=" O GLY I 223 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 280 Processing helix chain 'I' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE I 313 " --> pdb=" O SER I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 343 through 386 Processing helix chain 'I' and resid 386 through 396 removed outlier: 3.721A pdb=" N VAL I 390 " --> pdb=" O HIS I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 412 Processing helix chain 'I' and resid 414 through 423 Processing helix chain 'I' and resid 425 through 429 Processing helix chain 'I' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS I 436 " --> pdb=" O LEU I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 477 removed outlier: 3.706A pdb=" N VAL I 461 " --> pdb=" O LYS I 457 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 30 Processing helix chain 'J' and resid 40 through 53 Processing helix chain 'J' and resid 64 through 75 Processing helix chain 'J' and resid 79 through 91 Processing helix chain 'J' and resid 128 through 133 Processing helix chain 'J' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL J 166 " --> pdb=" O PRO J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 198 Processing helix chain 'J' and resid 202 through 208 Processing helix chain 'J' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE J 227 " --> pdb=" O GLY J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 280 Processing helix chain 'J' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE J 313 " --> pdb=" O SER J 309 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 386 Processing helix chain 'J' and resid 386 through 396 removed outlier: 3.720A pdb=" N VAL J 390 " --> pdb=" O HIS J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 399 through 412 Processing helix chain 'J' and resid 414 through 423 Processing helix chain 'J' and resid 425 through 429 Processing helix chain 'J' and resid 430 through 457 removed outlier: 4.202A pdb=" N LYS J 436 " --> pdb=" O LEU J 432 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL J 461 " --> pdb=" O LYS J 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 30 Processing helix chain 'K' and resid 40 through 53 Processing helix chain 'K' and resid 64 through 75 Processing helix chain 'K' and resid 79 through 91 Processing helix chain 'K' and resid 128 through 133 Processing helix chain 'K' and resid 162 through 168 removed outlier: 3.669A pdb=" N VAL K 166 " --> pdb=" O PRO K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 198 Processing helix chain 'K' and resid 202 through 208 Processing helix chain 'K' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE K 227 " --> pdb=" O GLY K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 280 Processing helix chain 'K' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE K 313 " --> pdb=" O SER K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 343 through 386 Processing helix chain 'K' and resid 386 through 396 removed outlier: 3.721A pdb=" N VAL K 390 " --> pdb=" O HIS K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 399 through 412 Processing helix chain 'K' and resid 414 through 423 Processing helix chain 'K' and resid 425 through 429 Processing helix chain 'K' and resid 430 through 457 removed outlier: 4.202A pdb=" N LYS K 436 " --> pdb=" O LEU K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL K 461 " --> pdb=" O LYS K 457 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 30 Processing helix chain 'L' and resid 40 through 53 Processing helix chain 'L' and resid 64 through 75 Processing helix chain 'L' and resid 79 through 91 Processing helix chain 'L' and resid 128 through 133 Processing helix chain 'L' and resid 162 through 168 removed outlier: 3.668A pdb=" N VAL L 166 " --> pdb=" O PRO L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 198 Processing helix chain 'L' and resid 202 through 208 Processing helix chain 'L' and resid 223 through 234 removed outlier: 3.732A pdb=" N ILE L 227 " --> pdb=" O GLY L 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 280 Processing helix chain 'L' and resid 309 through 321 removed outlier: 3.732A pdb=" N ILE L 313 " --> pdb=" O SER L 309 " (cutoff:3.500A) Processing helix chain 'L' and resid 343 through 386 Processing helix chain 'L' and resid 386 through 396 removed outlier: 3.720A pdb=" N VAL L 390 " --> pdb=" O HIS L 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 399 through 412 Processing helix chain 'L' and resid 414 through 423 Processing helix chain 'L' and resid 425 through 429 Processing helix chain 'L' and resid 430 through 457 removed outlier: 4.201A pdb=" N LYS L 436 " --> pdb=" O LEU L 432 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 477 removed outlier: 3.705A pdb=" N VAL L 461 " --> pdb=" O LYS L 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 143 through 145 Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 330 Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG A 243 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 288 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 332 through 335 Processing sheet with id=AA6, first strand: chain 'B' and resid 62 through 63 Processing sheet with id=AA7, first strand: chain 'B' and resid 143 through 145 Processing sheet with id=AA8, first strand: chain 'B' and resid 324 through 330 Processing sheet with id=AA9, first strand: chain 'B' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG B 243 " --> pdb=" O THR B 259 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B 288 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 332 through 335 Processing sheet with id=AB2, first strand: chain 'C' and resid 62 through 63 Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 145 Processing sheet with id=AB4, first strand: chain 'C' and resid 324 through 330 Processing sheet with id=AB5, first strand: chain 'C' and resid 243 through 247 removed outlier: 6.429A pdb=" N ARG C 243 " --> pdb=" O THR C 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 288 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 332 through 335 Processing sheet with id=AB7, first strand: chain 'D' and resid 62 through 63 Processing sheet with id=AB8, first strand: chain 'D' and resid 143 through 145 Processing sheet with id=AB9, first strand: chain 'D' and resid 324 through 330 Processing sheet with id=AC1, first strand: chain 'D' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG D 243 " --> pdb=" O THR D 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D 288 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 332 through 335 Processing sheet with id=AC3, first strand: chain 'E' and resid 62 through 63 Processing sheet with id=AC4, first strand: chain 'E' and resid 143 through 145 Processing sheet with id=AC5, first strand: chain 'E' and resid 324 through 330 Processing sheet with id=AC6, first strand: chain 'E' and resid 243 through 247 removed outlier: 6.429A pdb=" N ARG E 243 " --> pdb=" O THR E 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA E 288 " --> pdb=" O GLU E 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 332 through 335 Processing sheet with id=AC8, first strand: chain 'F' and resid 62 through 63 Processing sheet with id=AC9, first strand: chain 'F' and resid 143 through 145 Processing sheet with id=AD1, first strand: chain 'F' and resid 324 through 330 Processing sheet with id=AD2, first strand: chain 'F' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG F 243 " --> pdb=" O THR F 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA F 288 " --> pdb=" O GLU F 303 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 332 through 335 Processing sheet with id=AD4, first strand: chain 'G' and resid 62 through 63 Processing sheet with id=AD5, first strand: chain 'G' and resid 143 through 145 Processing sheet with id=AD6, first strand: chain 'G' and resid 324 through 330 Processing sheet with id=AD7, first strand: chain 'G' and resid 243 through 247 removed outlier: 6.427A pdb=" N ARG G 243 " --> pdb=" O THR G 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA G 288 " --> pdb=" O GLU G 303 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 332 through 335 Processing sheet with id=AD9, first strand: chain 'H' and resid 62 through 63 Processing sheet with id=AE1, first strand: chain 'H' and resid 143 through 145 Processing sheet with id=AE2, first strand: chain 'H' and resid 324 through 330 Processing sheet with id=AE3, first strand: chain 'H' and resid 243 through 247 removed outlier: 6.427A pdb=" N ARG H 243 " --> pdb=" O THR H 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA H 288 " --> pdb=" O GLU H 303 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 332 through 335 Processing sheet with id=AE5, first strand: chain 'I' and resid 62 through 63 Processing sheet with id=AE6, first strand: chain 'I' and resid 143 through 145 Processing sheet with id=AE7, first strand: chain 'I' and resid 324 through 330 Processing sheet with id=AE8, first strand: chain 'I' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG I 243 " --> pdb=" O THR I 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA I 288 " --> pdb=" O GLU I 303 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 332 through 335 Processing sheet with id=AF1, first strand: chain 'J' and resid 62 through 63 Processing sheet with id=AF2, first strand: chain 'J' and resid 143 through 145 Processing sheet with id=AF3, first strand: chain 'J' and resid 324 through 330 Processing sheet with id=AF4, first strand: chain 'J' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG J 243 " --> pdb=" O THR J 259 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA J 288 " --> pdb=" O GLU J 303 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 332 through 335 Processing sheet with id=AF6, first strand: chain 'K' and resid 62 through 63 Processing sheet with id=AF7, first strand: chain 'K' and resid 143 through 145 Processing sheet with id=AF8, first strand: chain 'K' and resid 324 through 330 Processing sheet with id=AF9, first strand: chain 'K' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG K 243 " --> pdb=" O THR K 259 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA K 288 " --> pdb=" O GLU K 303 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 332 through 335 Processing sheet with id=AG2, first strand: chain 'L' and resid 62 through 63 Processing sheet with id=AG3, first strand: chain 'L' and resid 143 through 145 Processing sheet with id=AG4, first strand: chain 'L' and resid 324 through 330 Processing sheet with id=AG5, first strand: chain 'L' and resid 243 through 247 removed outlier: 6.428A pdb=" N ARG L 243 " --> pdb=" O THR L 259 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA L 288 " --> pdb=" O GLU L 303 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 332 through 335 2676 hydrogen bonds defined for protein. 7740 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.99 Time building geometry restraints manager: 23.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15689 1.34 - 1.46: 8464 1.46 - 1.58: 22071 1.58 - 1.70: 0 1.70 - 1.82: 504 Bond restraints: 46728 Sorted by residual: bond pdb=" CB GLU G 131 " pdb=" CG GLU G 131 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CB GLU K 131 " pdb=" CG GLU K 131 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.93e+00 bond pdb=" CB GLU H 131 " pdb=" CG GLU H 131 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.91e+00 bond pdb=" CB GLU C 131 " pdb=" CG GLU C 131 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CB GLU B 131 " pdb=" CG GLU B 131 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.89e+00 ... (remaining 46723 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.06: 1069 106.06 - 113.05: 26215 113.05 - 120.04: 15854 120.04 - 127.02: 19466 127.02 - 134.01: 360 Bond angle restraints: 62964 Sorted by residual: angle pdb=" C TYR G 75 " pdb=" N HIS G 76 " pdb=" CA HIS G 76 " ideal model delta sigma weight residual 122.42 116.61 5.81 1.23e+00 6.61e-01 2.23e+01 angle pdb=" C TYR D 75 " pdb=" N HIS D 76 " pdb=" CA HIS D 76 " ideal model delta sigma weight residual 122.42 116.61 5.81 1.23e+00 6.61e-01 2.23e+01 angle pdb=" C TYR H 75 " pdb=" N HIS H 76 " pdb=" CA HIS H 76 " ideal model delta sigma weight residual 122.42 116.62 5.80 1.23e+00 6.61e-01 2.22e+01 angle pdb=" C TYR B 75 " pdb=" N HIS B 76 " pdb=" CA HIS B 76 " ideal model delta sigma weight residual 122.42 116.63 5.79 1.23e+00 6.61e-01 2.21e+01 angle pdb=" C TYR L 75 " pdb=" N HIS L 76 " pdb=" CA HIS L 76 " ideal model delta sigma weight residual 122.42 116.64 5.78 1.23e+00 6.61e-01 2.21e+01 ... (remaining 62959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.64: 27829 14.64 - 29.29: 1127 29.29 - 43.93: 120 43.93 - 58.58: 0 58.58 - 73.22: 12 Dihedral angle restraints: 29088 sinusoidal: 12216 harmonic: 16872 Sorted by residual: dihedral pdb=" CA ILE I 180 " pdb=" C ILE I 180 " pdb=" N PRO I 181 " pdb=" CA PRO I 181 " ideal model delta harmonic sigma weight residual 180.00 153.22 26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ILE J 180 " pdb=" C ILE J 180 " pdb=" N PRO J 181 " pdb=" CA PRO J 181 " ideal model delta harmonic sigma weight residual 180.00 153.25 26.75 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA ILE C 180 " pdb=" C ILE C 180 " pdb=" N PRO C 181 " pdb=" CA PRO C 181 " ideal model delta harmonic sigma weight residual 180.00 153.26 26.74 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 29085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 5448 0.059 - 0.119: 1494 0.119 - 0.178: 222 0.178 - 0.238: 12 0.238 - 0.297: 12 Chirality restraints: 7188 Sorted by residual: chirality pdb=" CB ILE D 302 " pdb=" CA ILE D 302 " pdb=" CG1 ILE D 302 " pdb=" CG2 ILE D 302 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE J 302 " pdb=" CA ILE J 302 " pdb=" CG1 ILE J 302 " pdb=" CG2 ILE J 302 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE L 302 " pdb=" CA ILE L 302 " pdb=" CG1 ILE L 302 " pdb=" CG2 ILE L 302 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 7185 not shown) Planarity restraints: 8172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE H 180 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO H 181 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO H 181 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 181 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 180 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO K 181 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO K 181 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 181 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 180 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO B 181 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " -0.034 5.00e-02 4.00e+02 ... (remaining 8169 not shown) Histogram of nonbonded interaction distances: 0.30 - 1.22: 84 1.22 - 2.14: 480 2.14 - 3.06: 29190 3.06 - 3.98: 123462 3.98 - 4.90: 217594 Warning: very small nonbonded interaction distances. Nonbonded interactions: 370810 Sorted by model distance: nonbonded pdb=" CG LEU D 6 " pdb=" CB VAL E 28 " model vdw 0.296 3.900 nonbonded pdb=" CB VAL J 28 " pdb=" CG LEU L 6 " model vdw 0.297 3.900 nonbonded pdb=" CG LEU B 6 " pdb=" CB VAL K 28 " model vdw 0.297 3.900 nonbonded pdb=" CB VAL D 28 " pdb=" CG LEU G 6 " model vdw 0.297 3.900 nonbonded pdb=" CG LEU E 6 " pdb=" CB VAL G 28 " model vdw 0.297 3.900 ... (remaining 370805 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 46044 46044 False True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 252 5.16 5 C 28896 2.51 5 N 8292 2.21 5 O 8604 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set model interpretation parameters: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.860 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.220 Process input model: 133.240 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.310 Internal consistency checks: 0.000 Total: 147.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.044 46728 Angle : 0.891 13.087 62964 Chirality : 0.054 0.297 7188 Planarity : 0.007 0.061 8172 Dihedral : 8.455 73.220 18144 Min Nonbonded Distance : 0.296 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.09), residues: 5772 helix: -1.41 (0.07), residues: 3072 sheet: -1.84 (0.25), residues: 312 loop : -2.54 (0.12), residues: 2388 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 786 time to evaluate : 6.131 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 786 average time/residue: 0.6192 time to fit residues: 496.0460 Evaluate side-chains 451 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 451 time to evaluate : 5.526 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 486 optimal weight: 8.9990 chunk 436 optimal weight: 0.9980 chunk 242 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 294 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 451 optimal weight: 7.9990 chunk 174 optimal weight: 30.0000 chunk 274 optimal weight: 0.9980 chunk 336 optimal weight: 30.0000 chunk 523 optimal weight: 5.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS A 316 ASN A 355 GLN ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS C 316 ASN C 355 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS D 316 ASN D 355 GLN E 78 HIS ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 316 ASN E 355 GLN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS F 316 ASN F 355 GLN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 HIS ** G 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 355 GLN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 HIS ** H 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 355 GLN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS I 316 ASN I 355 GLN ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 HIS J 316 ASN J 355 GLN K 43 HIS K 78 HIS ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 HIS ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 355 GLN L 78 HIS ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 HIS ** L 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 355 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.036 46728 Angle : 0.678 11.017 62964 Chirality : 0.045 0.207 7188 Planarity : 0.005 0.045 8172 Dihedral : 5.780 25.383 6384 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.11), residues: 5772 helix: 0.59 (0.09), residues: 3000 sheet: -1.57 (0.24), residues: 420 loop : -2.56 (0.13), residues: 2352 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 12 poor density : 517 time to evaluate : 6.014 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 517 average time/residue: 0.5875 time to fit residues: 313.2393 Evaluate side-chains 396 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 396 time to evaluate : 5.932 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 290 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 435 optimal weight: 3.9990 chunk 356 optimal weight: 0.4980 chunk 144 optimal weight: 9.9990 chunk 524 optimal weight: 9.9990 chunk 566 optimal weight: 8.9990 chunk 466 optimal weight: 6.9990 chunk 519 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 420 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN B 78 HIS ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 10 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 ASN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 HIS ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 10 ASN L 51 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.031 46728 Angle : 0.589 8.084 62964 Chirality : 0.042 0.196 7188 Planarity : 0.004 0.040 8172 Dihedral : 5.208 24.215 6384 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.11), residues: 5772 helix: 1.35 (0.09), residues: 3012 sheet: -1.27 (0.24), residues: 408 loop : -2.41 (0.13), residues: 2352 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 484 time to evaluate : 6.285 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.5775 time to fit residues: 289.5205 Evaluate side-chains 392 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 392 time to evaluate : 6.231 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.3449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 517 optimal weight: 2.9990 chunk 393 optimal weight: 0.0370 chunk 271 optimal weight: 9.9990 chunk 58 optimal weight: 30.0000 chunk 250 optimal weight: 0.4980 chunk 351 optimal weight: 3.9990 chunk 525 optimal weight: 9.9990 chunk 556 optimal weight: 0.0470 chunk 274 optimal weight: 0.8980 chunk 498 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 overall best weight: 0.8958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 316 ASN ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 10 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 ASN I 10 ASN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 ASN L 10 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 316 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.037 46728 Angle : 0.505 9.302 62964 Chirality : 0.041 0.236 7188 Planarity : 0.004 0.034 8172 Dihedral : 4.596 23.448 6384 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.12), residues: 5772 helix: 1.94 (0.10), residues: 3024 sheet: -1.80 (0.21), residues: 552 loop : -2.02 (0.14), residues: 2196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 516 time to evaluate : 6.140 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.5843 time to fit residues: 310.8671 Evaluate side-chains 396 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 396 time to evaluate : 5.883 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.8388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 463 optimal weight: 8.9990 chunk 316 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 414 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 475 optimal weight: 6.9990 chunk 384 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 284 optimal weight: 6.9990 chunk 499 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 51 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 HIS ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.045 46728 Angle : 0.734 15.310 62964 Chirality : 0.046 0.232 7188 Planarity : 0.005 0.060 8172 Dihedral : 5.572 27.038 6384 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.11), residues: 5772 helix: 1.38 (0.09), residues: 3024 sheet: -1.27 (0.23), residues: 468 loop : -2.20 (0.14), residues: 2280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 465 time to evaluate : 6.957 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.5931 time to fit residues: 285.7784 Evaluate side-chains 366 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 366 time to evaluate : 6.050 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.2359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 187 optimal weight: 10.0000 chunk 501 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 326 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 557 optimal weight: 5.9990 chunk 462 optimal weight: 2.9990 chunk 258 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 292 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 184 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.003 0.031 46728 Angle : 0.551 7.878 62964 Chirality : 0.042 0.237 7188 Planarity : 0.004 0.036 8172 Dihedral : 4.883 23.941 6384 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.12), residues: 5772 helix: 1.95 (0.10), residues: 3024 sheet: -1.67 (0.20), residues: 612 loop : -1.78 (0.15), residues: 2136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 483 time to evaluate : 6.020 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 484 average time/residue: 0.5771 time to fit residues: 289.2467 Evaluate side-chains 377 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 377 time to evaluate : 6.449 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.5060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 317 optimal weight: 3.9990 chunk 406 optimal weight: 7.9990 chunk 315 optimal weight: 10.0000 chunk 469 optimal weight: 5.9990 chunk 311 optimal weight: 9.9990 chunk 555 optimal weight: 20.0000 chunk 347 optimal weight: 0.5980 chunk 338 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 ASN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.038 46728 Angle : 0.646 11.057 62964 Chirality : 0.044 0.240 7188 Planarity : 0.004 0.049 8172 Dihedral : 5.243 27.140 6384 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.12), residues: 5772 helix: 1.70 (0.10), residues: 3036 sheet: -1.04 (0.24), residues: 468 loop : -1.95 (0.14), residues: 2268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 457 time to evaluate : 5.910 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.5802 time to fit residues: 274.7075 Evaluate side-chains 363 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 363 time to evaluate : 6.096 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.3760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 9.9990 chunk 221 optimal weight: 20.0000 chunk 331 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 352 optimal weight: 3.9990 chunk 378 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 436 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 ASN C 355 GLN D 5 ASN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 355 GLN ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 ASN K 51 ASN ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.033 46728 Angle : 0.619 9.560 62964 Chirality : 0.044 0.248 7188 Planarity : 0.004 0.044 8172 Dihedral : 5.145 26.265 6384 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.12), residues: 5772 helix: 1.72 (0.10), residues: 3024 sheet: -1.47 (0.21), residues: 612 loop : -1.76 (0.14), residues: 2136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 457 time to evaluate : 6.056 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.5927 time to fit residues: 280.5799 Evaluate side-chains 375 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 375 time to evaluate : 6.321 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.4433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 505 optimal weight: 10.0000 chunk 531 optimal weight: 7.9990 chunk 485 optimal weight: 4.9990 chunk 517 optimal weight: 5.9990 chunk 311 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 chunk 406 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 467 optimal weight: 10.0000 chunk 489 optimal weight: 0.9980 chunk 515 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 ASN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.035 46728 Angle : 0.611 8.741 62964 Chirality : 0.044 0.215 7188 Planarity : 0.004 0.054 8172 Dihedral : 5.084 26.561 6384 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.12), residues: 5772 helix: 1.79 (0.10), residues: 3024 sheet: -1.38 (0.21), residues: 612 loop : -1.80 (0.14), residues: 2136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 459 time to evaluate : 6.378 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.5933 time to fit residues: 282.1600 Evaluate side-chains 372 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 372 time to evaluate : 5.477 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 5.9990 chunk 547 optimal weight: 0.9990 chunk 333 optimal weight: 0.9980 chunk 259 optimal weight: 0.3980 chunk 380 optimal weight: 7.9990 chunk 573 optimal weight: 8.9990 chunk 528 optimal weight: 0.8980 chunk 456 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 352 optimal weight: 1.9990 chunk 280 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 HIS ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 HIS ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.030 46728 Angle : 0.528 8.937 62964 Chirality : 0.042 0.256 7188 Planarity : 0.004 0.039 8172 Dihedral : 4.595 24.531 6384 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.12), residues: 5772 helix: 2.10 (0.10), residues: 3084 sheet: -0.71 (0.25), residues: 468 loop : -1.78 (0.14), residues: 2220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield and 0 Emsley and 5772 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 517 time to evaluate : 5.652 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.5997 time to fit residues: 319.4562 Evaluate side-chains 387 residues out of total 5016 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 387 time to evaluate : 6.269 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.9716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 362 optimal weight: 5.9990 chunk 486 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 421 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 457 optimal weight: 0.0980 chunk 191 optimal weight: 4.9990 chunk 469 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN F 51 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.107522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.093041 restraints weight = 204142.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.094511 restraints weight = 146675.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.095880 restraints weight = 97282.543| |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.002 0.067 46728 ANGLE : 0.535 7.880 62964 CHIRALITY : 0.042 0.217 7188 PLANARITY : 0.004 0.045 8172 DIHEDRAL : 4.501 25.572 6384 MIN NONBONDED DISTANCE : 2.152 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 13.22 RAMACHANDRAN PLOT: OUTLIERS : 0.00 % ALLOWED : 5.25 % FAVORED : 94.75 % ROTAMER OUTLIERS : 0.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 0.00 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 0.00 % TWISTED GENERAL : 0.00 % RAMA-Z (RAMACHANDRAN PLOT Z-SCORE): INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD |RAMA-Z| < 2. SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY; THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER. WHOLE: 0.86 (0.12), RESIDUES: 5772 HELIX: 2.39 (0.10), RESIDUES: 2988 SHEET: -0.99 (0.23), RESIDUES: 552 LOOP : -1.64 (0.14), RESIDUES: 2232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.002 0.067 46728 Angle : 0.535 7.880 62964 Chirality : 0.042 0.217 7188 Planarity : 0.004 0.045 8172 Dihedral : 4.501 25.572 6384 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.12), residues: 5772 helix: 2.39 (0.10), residues: 2988 sheet: -0.99 (0.23), residues: 552 loop : -1.64 (0.14), residues: 2232 =============================================================================== Job complete usr+sys time: 7502.98 seconds wall clock time: 140 minutes 12.05 seconds (8412.05 seconds total)