Starting phenix.real_space_refine on Mon Mar 25 03:21:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1r_9318/03_2024/6n1r_9318_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1r_9318/03_2024/6n1r_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_9318/03_2024/6n1r_9318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1r_9318/03_2024/6n1r_9318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1r_9318/03_2024/6n1r_9318_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n1r_9318/03_2024/6n1r_9318_neut.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. Process input model Symmetric amino acids flipped Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A ARG 295": "NH1" <-> "NH2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B ARG 282": "NH1" <-> "NH2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ARG 295": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "C ARG 276": "NH1" <-> "NH2" Residue "C ARG 282": "NH1" <-> "NH2" Residue "C ARG 290": "NH1" <-> "NH2" Residue "C ARG 295": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C ARG 395": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "D ARG 276": "NH1" <-> "NH2" Residue "D ARG 282": "NH1" <-> "NH2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "D ARG 295": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D ARG 392": "NH1" <-> "NH2" Residue "D ARG 395": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "E ARG 276": "NH1" <-> "NH2" Residue "E ARG 282": "NH1" <-> "NH2" Residue "E ARG 290": "NH1" <-> "NH2" Residue "E ARG 295": "NH1" <-> "NH2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E ARG 392": "NH1" <-> "NH2" Residue "E ARG 395": "NH1" <-> "NH2" Residue "E ARG 416": "NH1" <-> "NH2" Residue "F ARG 276": "NH1" <-> "NH2" Residue "F ARG 282": "NH1" <-> "NH2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F ARG 295": "NH1" <-> "NH2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F ARG 392": "NH1" <-> "NH2" Residue "F ARG 395": "NH1" <-> "NH2" Residue "F ARG 416": "NH1" <-> "NH2" Residue "G ARG 276": "NH1" <-> "NH2" Residue "G ARG 282": "NH1" <-> "NH2" Residue "G ARG 290": "NH1" <-> "NH2" Residue "G ARG 295": "NH1" <-> "NH2" Residue "G ARG 306": "NH1" <-> "NH2" Residue "G ARG 392": "NH1" <-> "NH2" Residue "G ARG 395": "NH1" <-> "NH2" Residue "G ARG 416": "NH1" <-> "NH2" Residue "H ARG 276": "NH1" <-> "NH2" Residue "H ARG 282": "NH1" <-> "NH2" Residue "H ARG 290": "NH1" <-> "NH2" Residue "H ARG 295": "NH1" <-> "NH2" Residue "H ARG 306": "NH1" <-> "NH2" Residue "H ARG 392": "NH1" <-> "NH2" Residue "H ARG 395": "NH1" <-> "NH2" Residue "H ARG 416": "NH1" <-> "NH2" Residue "I ARG 276": "NH1" <-> "NH2" Residue "I ARG 282": "NH1" <-> "NH2" Residue "I ARG 290": "NH1" <-> "NH2" Residue "I ARG 295": "NH1" <-> "NH2" Residue "I ARG 306": "NH1" <-> "NH2" Residue "I ARG 392": "NH1" <-> "NH2" Residue "I ARG 395": "NH1" <-> "NH2" Residue "I ARG 416": "NH1" <-> "NH2" Residue "J ARG 276": "NH1" <-> "NH2" Residue "J ARG 282": "NH1" <-> "NH2" Residue "J ARG 290": "NH1" <-> "NH2" Residue "J ARG 295": "NH1" <-> "NH2" Residue "J ARG 306": "NH1" <-> "NH2" Residue "J ARG 392": "NH1" <-> "NH2" Residue "J ARG 395": "NH1" <-> "NH2" Residue "J ARG 416": "NH1" <-> "NH2" Residue "K ARG 276": "NH1" <-> "NH2" Residue "K ARG 282": "NH1" <-> "NH2" Residue "K ARG 290": "NH1" <-> "NH2" Residue "K ARG 295": "NH1" <-> "NH2" Residue "K ARG 306": "NH1" <-> "NH2" Residue "K ARG 392": "NH1" <-> "NH2" Residue "K ARG 395": "NH1" <-> "NH2" Residue "K ARG 416": "NH1" <-> "NH2" Residue "L ARG 276": "NH1" <-> "NH2" Residue "L ARG 282": "NH1" <-> "NH2" Residue "L ARG 290": "NH1" <-> "NH2" Residue "L ARG 295": "NH1" <-> "NH2" Residue "L ARG 306": "NH1" <-> "NH2" Residue "L ARG 392": "NH1" <-> "NH2" Residue "L ARG 395": "NH1" <-> "NH2" Residue "L ARG 416": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 21.86, per 1000 atoms: 0.47 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 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.58 Conformation dependent library (CDL) restraints added in 7.8 seconds 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. 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: 4.58 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: 18.33 Time building geometry restraints manager: 18.06 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. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 6.850 Check model and map are aligned: 0.560 Set scattering table: 0.400 Process input model: 111.410 Find NCS groups from input model: 3.210 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 46728 Z= 0.389 Angle : 0.891 13.087 62964 Z= 0.511 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 : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 94 HIS 0.013 0.003 HIS G 183 PHE 0.023 0.003 PHE F 300 TYR 0.021 0.004 TYR B 96 ARG 0.005 0.001 ARG C 428 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 786 time to evaluate : 5.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7688 (mmm) cc_final: 0.7370 (mmm) REVERT: A 342 LEU cc_start: 0.8472 (mt) cc_final: 0.7925 (mp) REVERT: B 132 MET cc_start: 0.7641 (mmm) cc_final: 0.7122 (mmm) REVERT: B 342 LEU cc_start: 0.8316 (mt) cc_final: 0.7741 (mp) REVERT: B 485 MET cc_start: 0.5883 (ptm) cc_final: 0.5598 (ppp) REVERT: C 132 MET cc_start: 0.7623 (mmm) cc_final: 0.7183 (mmm) REVERT: C 342 LEU cc_start: 0.8540 (mt) cc_final: 0.7969 (mp) REVERT: D 15 MET cc_start: 0.8363 (ptm) cc_final: 0.8102 (ptp) REVERT: D 132 MET cc_start: 0.7705 (mmm) cc_final: 0.7391 (mmm) REVERT: D 485 MET cc_start: 0.5802 (ptm) cc_final: 0.5601 (ppp) REVERT: E 132 MET cc_start: 0.7700 (mmm) cc_final: 0.7392 (mmm) REVERT: E 342 LEU cc_start: 0.8541 (mt) cc_final: 0.8003 (mp) REVERT: E 485 MET cc_start: 0.5764 (ptm) cc_final: 0.5267 (ppp) REVERT: F 15 MET cc_start: 0.8594 (ptm) cc_final: 0.8229 (ptp) REVERT: F 132 MET cc_start: 0.7686 (mmm) cc_final: 0.7234 (mmm) REVERT: G 15 MET cc_start: 0.8484 (ptm) cc_final: 0.7840 (ptp) REVERT: H 132 MET cc_start: 0.7871 (mmm) cc_final: 0.7609 (mmm) REVERT: H 485 MET cc_start: 0.5702 (ptm) cc_final: 0.5425 (ppp) REVERT: I 15 MET cc_start: 0.8446 (ptm) cc_final: 0.8220 (ptm) REVERT: J 15 MET cc_start: 0.8331 (ptm) cc_final: 0.8077 (ptm) REVERT: J 132 MET cc_start: 0.7838 (mmm) cc_final: 0.7500 (mmm) REVERT: K 15 MET cc_start: 0.8465 (ptm) cc_final: 0.8079 (ptp) REVERT: K 132 MET cc_start: 0.7746 (mmm) cc_final: 0.7366 (mmm) REVERT: K 342 LEU cc_start: 0.8569 (mt) cc_final: 0.8057 (mp) REVERT: K 485 MET cc_start: 0.5329 (ptm) cc_final: 0.5094 (ppp) REVERT: L 15 MET cc_start: 0.8355 (ptm) cc_final: 0.8098 (ptm) REVERT: L 72 MET cc_start: 0.6204 (mmm) cc_final: 0.5973 (mmm) REVERT: L 132 MET cc_start: 0.7852 (mmm) cc_final: 0.7592 (mmm) outliers start: 0 outliers final: 0 residues processed: 786 average time/residue: 0.5682 time to fit residues: 731.5154 Evaluate side-chains 453 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 5.543 ------------------------------------------------------------------------------- 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: 20.0000 chunk 436 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 294 optimal weight: 8.9990 chunk 233 optimal weight: 8.9990 chunk 451 optimal weight: 2.9990 chunk 174 optimal weight: 40.0000 chunk 274 optimal weight: 0.5980 chunk 336 optimal weight: 10.0000 chunk 523 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 78 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 183 HIS B 316 ASN C 51 ASN ** 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 51 ASN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS D 316 ASN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS F 316 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** G 183 HIS G 316 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 HIS H 316 ASN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS I 316 ASN J 43 HIS J 51 ASN ** 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 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 78 HIS ** 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 183 HIS K 316 ASN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 HIS ** 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 183 HIS L 316 ASN L 355 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 46728 Z= 0.229 Angle : 0.665 9.285 62964 Z= 0.354 Chirality : 0.045 0.200 7188 Planarity : 0.005 0.046 8172 Dihedral : 5.725 25.789 6384 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.16 % Allowed : 7.14 % Favored : 91.71 % 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: -1.19 (0.11), residues: 5772 helix: 0.64 (0.09), residues: 2976 sheet: -2.44 (0.18), residues: 696 loop : -2.27 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 94 HIS 0.004 0.001 HIS I 183 PHE 0.015 0.002 PHE A 300 TYR 0.015 0.002 TYR F 351 ARG 0.007 0.001 ARG G 480 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 505 time to evaluate : 5.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 MET cc_start: 0.8381 (ptm) cc_final: 0.7713 (ptm) REVERT: B 50 MET cc_start: 0.7501 (mtm) cc_final: 0.7148 (mtm) REVERT: B 222 MET cc_start: 0.6361 (mtt) cc_final: 0.5909 (mtt) REVERT: C 15 MET cc_start: 0.8428 (ptm) cc_final: 0.8153 (ptp) REVERT: D 15 MET cc_start: 0.8299 (ptm) cc_final: 0.8045 (ptp) REVERT: E 15 MET cc_start: 0.8160 (ptm) cc_final: 0.7953 (ptp) REVERT: F 15 MET cc_start: 0.8313 (ptm) cc_final: 0.8002 (ptm) REVERT: I 22 TYR cc_start: 0.6992 (t80) cc_final: 0.6792 (t80) REVERT: J 15 MET cc_start: 0.8277 (ptm) cc_final: 0.7948 (ptp) REVERT: J 22 TYR cc_start: 0.6734 (t80) cc_final: 0.6498 (t80) REVERT: K 15 MET cc_start: 0.8215 (ptm) cc_final: 0.7986 (ptp) REVERT: K 19 PHE cc_start: 0.7355 (t80) cc_final: 0.6981 (t80) REVERT: K 72 MET cc_start: 0.6209 (mmm) cc_final: 0.5995 (mmm) REVERT: L 15 MET cc_start: 0.8208 (ptm) cc_final: 0.7907 (ptp) REVERT: L 72 MET cc_start: 0.6161 (mmm) cc_final: 0.5936 (mmm) REVERT: L 485 MET cc_start: 0.6085 (ptm) cc_final: 0.5630 (ppp) outliers start: 58 outliers final: 15 residues processed: 547 average time/residue: 0.5130 time to fit residues: 480.1381 Evaluate side-chains 423 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 408 time to evaluate : 5.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 8 ASN Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain G residue 8 ASN Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 8 ASN Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain L residue 8 ASN Chi-restraints excluded: chain L residue 409 SER Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP 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: 0.9990 chunk 435 optimal weight: 3.9990 chunk 356 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 524 optimal weight: 6.9990 chunk 566 optimal weight: 6.9990 chunk 466 optimal weight: 0.6980 chunk 519 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 420 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 78 HIS ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN C 10 ASN C 51 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN D 51 ASN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 GLN E 10 ASN E 51 ASN ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN F 10 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 GLN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 355 GLN H 10 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 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 355 GLN J 10 ASN J 51 ASN ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 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 L 10 ASN ** L 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 46728 Z= 0.161 Angle : 0.578 8.910 62964 Z= 0.307 Chirality : 0.043 0.187 7188 Planarity : 0.004 0.038 8172 Dihedral : 5.075 25.614 6384 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.40 % Allowed : 8.03 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.11), residues: 5772 helix: 1.30 (0.09), residues: 2976 sheet: -2.38 (0.17), residues: 708 loop : -2.18 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 94 HIS 0.003 0.001 HIS K 228 PHE 0.012 0.001 PHE A 300 TYR 0.012 0.002 TYR F 231 ARG 0.006 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 458 time to evaluate : 5.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8956 (p0) cc_final: 0.8390 (t0) REVERT: B 15 MET cc_start: 0.8391 (ptm) cc_final: 0.7543 (ptm) REVERT: B 50 MET cc_start: 0.7660 (mtm) cc_final: 0.6992 (mtm) REVERT: C 50 MET cc_start: 0.7819 (mtm) cc_final: 0.7612 (mtm) REVERT: D 15 MET cc_start: 0.8313 (ptm) cc_final: 0.7942 (ptp) REVERT: E 15 MET cc_start: 0.8230 (ptm) cc_final: 0.7945 (ptp) REVERT: F 50 MET cc_start: 0.7859 (mtm) cc_final: 0.7437 (mtm) REVERT: F 174 VAL cc_start: 0.5501 (OUTLIER) cc_final: 0.5241 (t) REVERT: F 485 MET cc_start: 0.5801 (ppp) cc_final: 0.5449 (ppp) REVERT: G 15 MET cc_start: 0.8477 (ptm) cc_final: 0.8255 (ptm) REVERT: G 37 ASP cc_start: 0.8951 (p0) cc_final: 0.8470 (t0) REVERT: G 207 MET cc_start: 0.8270 (mmm) cc_final: 0.7793 (mmm) REVERT: H 15 MET cc_start: 0.8375 (ptm) cc_final: 0.8126 (ptm) REVERT: H 174 VAL cc_start: 0.5472 (OUTLIER) cc_final: 0.5267 (t) REVERT: I 22 TYR cc_start: 0.7017 (t80) cc_final: 0.6499 (t80) REVERT: I 24 MET cc_start: 0.7609 (ttm) cc_final: 0.7136 (ttm) REVERT: I 50 MET cc_start: 0.7763 (mtm) cc_final: 0.7340 (mtm) REVERT: I 207 MET cc_start: 0.8099 (mtp) cc_final: 0.7844 (tpt) REVERT: J 15 MET cc_start: 0.8319 (ptm) cc_final: 0.8005 (ptp) REVERT: J 320 MET cc_start: 0.8058 (tpp) cc_final: 0.7703 (tpp) REVERT: K 15 MET cc_start: 0.8370 (ptm) cc_final: 0.8110 (ptp) REVERT: K 19 PHE cc_start: 0.7169 (t80) cc_final: 0.6810 (t80) REVERT: K 72 MET cc_start: 0.6207 (mmm) cc_final: 0.5897 (mmm) REVERT: L 15 MET cc_start: 0.8268 (ptm) cc_final: 0.7923 (ptp) outliers start: 70 outliers final: 19 residues processed: 505 average time/residue: 0.4965 time to fit residues: 432.1604 Evaluate side-chains 421 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 400 time to evaluate : 5.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 517 optimal weight: 5.9990 chunk 393 optimal weight: 9.9990 chunk 271 optimal weight: 6.9990 chunk 58 optimal weight: 40.0000 chunk 250 optimal weight: 50.0000 chunk 351 optimal weight: 6.9990 chunk 525 optimal weight: 9.9990 chunk 556 optimal weight: 20.0000 chunk 274 optimal weight: 0.6980 chunk 498 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- 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 51 ASN ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 51 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 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** G 10 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 10 ASN I 51 ASN ** I 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 HIS ** J 51 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** L 51 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 46728 Z= 0.310 Angle : 0.671 7.505 62964 Z= 0.358 Chirality : 0.045 0.307 7188 Planarity : 0.005 0.041 8172 Dihedral : 5.372 24.422 6384 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 1.71 % Allowed : 9.87 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.12), residues: 5772 helix: 1.23 (0.09), residues: 3036 sheet: -2.18 (0.20), residues: 564 loop : -2.13 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 93 HIS 0.004 0.001 HIS D 78 PHE 0.021 0.002 PHE A 300 TYR 0.018 0.002 TYR G 351 ARG 0.007 0.001 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 413 time to evaluate : 5.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.7950 (ptp) cc_final: 0.7598 (ptm) REVERT: A 132 MET cc_start: 0.7537 (tpp) cc_final: 0.7234 (mmm) REVERT: A 485 MET cc_start: 0.4624 (ptt) cc_final: 0.3984 (ptt) REVERT: B 15 MET cc_start: 0.8503 (ptm) cc_final: 0.7699 (ptm) REVERT: B 50 MET cc_start: 0.7474 (mtm) cc_final: 0.7072 (mtm) REVERT: C 125 MET cc_start: 0.7013 (ttm) cc_final: 0.6726 (mtt) REVERT: C 207 MET cc_start: 0.8202 (mmm) cc_final: 0.7732 (mmm) REVERT: D 15 MET cc_start: 0.8386 (ptm) cc_final: 0.7953 (ptp) REVERT: D 99 MET cc_start: 0.6870 (tpp) cc_final: 0.6659 (tpp) REVERT: E 15 MET cc_start: 0.8302 (ptm) cc_final: 0.8001 (ptp) REVERT: E 132 MET cc_start: 0.7384 (tpp) cc_final: 0.7044 (mmm) REVERT: E 450 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6865 (t70) REVERT: F 15 MET cc_start: 0.8388 (ptm) cc_final: 0.8029 (ptm) REVERT: F 50 MET cc_start: 0.7747 (mtm) cc_final: 0.7444 (mtm) REVERT: F 320 MET cc_start: 0.7924 (tpp) cc_final: 0.7663 (tpp) REVERT: G 15 MET cc_start: 0.8547 (ptm) cc_final: 0.8281 (ptm) REVERT: G 22 TYR cc_start: 0.6349 (OUTLIER) cc_final: 0.5896 (t80) REVERT: H 99 MET cc_start: 0.6458 (tpp) cc_final: 0.6062 (tpp) REVERT: I 22 TYR cc_start: 0.7157 (t80) cc_final: 0.6950 (t80) REVERT: I 24 MET cc_start: 0.7750 (ttm) cc_final: 0.7306 (ttm) REVERT: I 50 MET cc_start: 0.7813 (mtm) cc_final: 0.7367 (mtm) REVERT: J 15 MET cc_start: 0.8501 (ptm) cc_final: 0.8105 (ptp) REVERT: J 99 MET cc_start: 0.6589 (tpp) cc_final: 0.6078 (tpp) REVERT: J 207 MET cc_start: 0.7910 (mmm) cc_final: 0.7680 (mmm) REVERT: J 320 MET cc_start: 0.8166 (tpp) cc_final: 0.7729 (tpp) REVERT: K 15 MET cc_start: 0.8444 (ptm) cc_final: 0.8082 (ptp) REVERT: K 22 TYR cc_start: 0.6545 (OUTLIER) cc_final: 0.5517 (t80) REVERT: K 207 MET cc_start: 0.8134 (mmm) cc_final: 0.7667 (mmm) REVERT: L 15 MET cc_start: 0.8384 (ptm) cc_final: 0.7907 (ptp) REVERT: L 72 MET cc_start: 0.6444 (mmm) cc_final: 0.6228 (mmm) REVERT: L 408 MET cc_start: 0.7150 (mmp) cc_final: 0.6649 (mmp) outliers start: 86 outliers final: 28 residues processed: 480 average time/residue: 0.5097 time to fit residues: 423.5875 Evaluate side-chains 423 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 392 time to evaluate : 5.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 463 optimal weight: 10.0000 chunk 316 optimal weight: 8.9990 chunk 8 optimal weight: 7.9990 chunk 414 optimal weight: 20.0000 chunk 229 optimal weight: 9.9990 chunk 475 optimal weight: 9.9990 chunk 384 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 284 optimal weight: 5.9990 chunk 499 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 51 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 51 ASN ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 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** ** 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** J 51 ASN ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 HIS ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 46728 Z= 0.288 Angle : 0.659 13.175 62964 Z= 0.353 Chirality : 0.045 0.202 7188 Planarity : 0.005 0.044 8172 Dihedral : 5.296 26.318 6384 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.41 % Allowed : 9.27 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.11), residues: 5772 helix: 1.21 (0.09), residues: 3036 sheet: -2.06 (0.20), residues: 552 loop : -2.10 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 93 HIS 0.004 0.001 HIS F 354 PHE 0.027 0.002 PHE K 19 TYR 0.018 0.002 TYR G 351 ARG 0.007 0.000 ARG G 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 404 time to evaluate : 5.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.7546 (tpp) cc_final: 0.7262 (mmm) REVERT: A 485 MET cc_start: 0.4492 (ptt) cc_final: 0.3880 (ptt) REVERT: B 15 MET cc_start: 0.8216 (ptm) cc_final: 0.7949 (ptm) REVERT: B 50 MET cc_start: 0.7592 (mtm) cc_final: 0.7011 (mtm) REVERT: C 22 TYR cc_start: 0.6632 (OUTLIER) cc_final: 0.5553 (t80) REVERT: C 125 MET cc_start: 0.7071 (ttm) cc_final: 0.6852 (mtt) REVERT: D 15 MET cc_start: 0.8387 (ptm) cc_final: 0.7896 (ptp) REVERT: D 50 MET cc_start: 0.7717 (mtm) cc_final: 0.7459 (mtm) REVERT: D 176 MET cc_start: 0.6788 (mtm) cc_final: 0.6495 (mtm) REVERT: E 15 MET cc_start: 0.8314 (ptm) cc_final: 0.7988 (ptp) REVERT: E 450 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6853 (t70) REVERT: F 15 MET cc_start: 0.8397 (ptm) cc_final: 0.7937 (ptm) REVERT: F 50 MET cc_start: 0.7725 (mtm) cc_final: 0.7381 (mtm) REVERT: F 408 MET cc_start: 0.7193 (mmt) cc_final: 0.6953 (mmt) REVERT: G 15 MET cc_start: 0.8521 (ptm) cc_final: 0.8219 (ptm) REVERT: G 22 TYR cc_start: 0.6267 (OUTLIER) cc_final: 0.5643 (t80) REVERT: G 99 MET cc_start: 0.6881 (tpp) cc_final: 0.6658 (tpp) REVERT: H 99 MET cc_start: 0.6417 (tpp) cc_final: 0.5991 (tpp) REVERT: H 176 MET cc_start: 0.7197 (OUTLIER) cc_final: 0.6487 (mtm) REVERT: I 22 TYR cc_start: 0.7148 (t80) cc_final: 0.6890 (t80) REVERT: I 24 MET cc_start: 0.7818 (ttm) cc_final: 0.7325 (ttm) REVERT: I 50 MET cc_start: 0.7793 (mtm) cc_final: 0.7310 (mtm) REVERT: J 15 MET cc_start: 0.8489 (ptm) cc_final: 0.8051 (ptp) REVERT: J 99 MET cc_start: 0.6683 (tpp) cc_final: 0.6263 (tpp) REVERT: J 264 MET cc_start: 0.8361 (mmt) cc_final: 0.8066 (mmt) REVERT: J 408 MET cc_start: 0.7206 (mmt) cc_final: 0.6803 (mmm) REVERT: K 15 MET cc_start: 0.8465 (ptm) cc_final: 0.8088 (ptm) REVERT: K 22 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.5377 (t80) REVERT: K 72 MET cc_start: 0.6369 (mmm) cc_final: 0.6061 (mmm) REVERT: L 15 MET cc_start: 0.8484 (ptm) cc_final: 0.8007 (ptm) REVERT: L 72 MET cc_start: 0.6420 (mmm) cc_final: 0.6102 (mmm) REVERT: L 408 MET cc_start: 0.7080 (mmp) cc_final: 0.6724 (mmp) outliers start: 121 outliers final: 61 residues processed: 489 average time/residue: 0.5048 time to fit residues: 426.5861 Evaluate side-chains 453 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 387 time to evaluate : 5.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 207 MET Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 187 optimal weight: 0.9990 chunk 501 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 326 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 557 optimal weight: 7.9990 chunk 462 optimal weight: 5.9990 chunk 258 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 292 optimal weight: 0.6980 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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** ** 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** ** 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 51 ASN ** 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 46728 Z= 0.206 Angle : 0.611 13.582 62964 Z= 0.323 Chirality : 0.043 0.202 7188 Planarity : 0.004 0.038 8172 Dihedral : 5.011 27.136 6384 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.21 % Allowed : 9.65 % Favored : 88.14 % 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: -0.18 (0.12), residues: 5772 helix: 1.50 (0.09), residues: 3036 sheet: -1.84 (0.21), residues: 552 loop : -2.05 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 93 HIS 0.003 0.001 HIS F 354 PHE 0.022 0.002 PHE K 19 TYR 0.015 0.002 TYR I 351 ARG 0.008 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 401 time to evaluate : 5.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.7553 (tpp) cc_final: 0.7183 (mmm) REVERT: A 408 MET cc_start: 0.5908 (mmm) cc_final: 0.5445 (mmm) REVERT: A 485 MET cc_start: 0.4500 (ptt) cc_final: 0.4058 (ppp) REVERT: B 50 MET cc_start: 0.7609 (mtm) cc_final: 0.6989 (mtm) REVERT: C 22 TYR cc_start: 0.6520 (OUTLIER) cc_final: 0.5342 (t80) REVERT: C 125 MET cc_start: 0.6914 (ttm) cc_final: 0.6683 (mtt) REVERT: C 207 MET cc_start: 0.8196 (mmm) cc_final: 0.7697 (mmm) REVERT: C 485 MET cc_start: 0.5849 (ppp) cc_final: 0.5423 (ppp) REVERT: D 15 MET cc_start: 0.8268 (ptm) cc_final: 0.7760 (ptp) REVERT: D 99 MET cc_start: 0.6828 (tpp) cc_final: 0.6590 (tpp) REVERT: E 15 MET cc_start: 0.8295 (ptm) cc_final: 0.7959 (ptp) REVERT: E 50 MET cc_start: 0.8047 (mpp) cc_final: 0.7826 (mpp) REVERT: E 408 MET cc_start: 0.6677 (mmt) cc_final: 0.6225 (mmm) REVERT: E 450 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6797 (t70) REVERT: F 15 MET cc_start: 0.8455 (ptm) cc_final: 0.8024 (ptm) REVERT: F 50 MET cc_start: 0.7806 (mtm) cc_final: 0.7318 (mtm) REVERT: F 207 MET cc_start: 0.8150 (mmm) cc_final: 0.7876 (mmm) REVERT: F 264 MET cc_start: 0.8108 (mmm) cc_final: 0.7677 (mmt) REVERT: F 408 MET cc_start: 0.7045 (mmt) cc_final: 0.6730 (mmt) REVERT: G 15 MET cc_start: 0.8445 (ptm) cc_final: 0.8159 (ptm) REVERT: G 99 MET cc_start: 0.6963 (tpp) cc_final: 0.6695 (tpp) REVERT: H 176 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6439 (mtm) REVERT: H 207 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7885 (mtm) REVERT: I 6 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6826 (pt) REVERT: I 22 TYR cc_start: 0.6995 (t80) cc_final: 0.6584 (t80) REVERT: I 24 MET cc_start: 0.7803 (ttm) cc_final: 0.7307 (ttm) REVERT: I 50 MET cc_start: 0.7794 (mtm) cc_final: 0.7282 (mtm) REVERT: J 15 MET cc_start: 0.8436 (ptm) cc_final: 0.8000 (ptp) REVERT: J 99 MET cc_start: 0.6654 (tpp) cc_final: 0.6310 (tpp) REVERT: J 264 MET cc_start: 0.8353 (mmt) cc_final: 0.8143 (mmt) REVERT: J 320 MET cc_start: 0.8212 (tpp) cc_final: 0.7660 (tpp) REVERT: J 408 MET cc_start: 0.7245 (mmt) cc_final: 0.6910 (mmm) REVERT: K 15 MET cc_start: 0.8461 (ptm) cc_final: 0.8089 (ptm) REVERT: K 22 TYR cc_start: 0.6364 (OUTLIER) cc_final: 0.5296 (t80) REVERT: K 408 MET cc_start: 0.6910 (mmt) cc_final: 0.6612 (mmm) REVERT: K 485 MET cc_start: 0.6043 (ppp) cc_final: 0.5603 (ppp) REVERT: L 6 LEU cc_start: 0.6303 (mt) cc_final: 0.5847 (pp) REVERT: L 15 MET cc_start: 0.8422 (ptm) cc_final: 0.8074 (ptm) REVERT: L 72 MET cc_start: 0.6256 (mmm) cc_final: 0.5930 (mmm) REVERT: L 408 MET cc_start: 0.6880 (mmp) cc_final: 0.6591 (mmp) REVERT: L 485 MET cc_start: 0.6285 (ppp) cc_final: 0.5981 (ppp) outliers start: 111 outliers final: 68 residues processed: 480 average time/residue: 0.5127 time to fit residues: 425.7325 Evaluate side-chains 467 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 393 time to evaluate : 4.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 207 MET Chi-restraints excluded: chain H residue 261 PHE Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 317 optimal weight: 40.0000 chunk 406 optimal weight: 9.9990 chunk 315 optimal weight: 20.0000 chunk 469 optimal weight: 5.9990 chunk 311 optimal weight: 8.9990 chunk 555 optimal weight: 20.0000 chunk 347 optimal weight: 20.0000 chunk 338 optimal weight: 3.9990 chunk 256 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 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** C 10 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** ** 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 46728 Z= 0.272 Angle : 0.659 13.443 62964 Z= 0.347 Chirality : 0.044 0.246 7188 Planarity : 0.004 0.041 8172 Dihedral : 5.150 29.174 6384 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 2.73 % Allowed : 9.73 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.12), residues: 5772 helix: 1.46 (0.09), residues: 3036 sheet: -1.74 (0.21), residues: 552 loop : -2.02 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 93 HIS 0.004 0.001 HIS F 354 PHE 0.043 0.002 PHE K 19 TYR 0.017 0.002 TYR I 351 ARG 0.010 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 394 time to evaluate : 5.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.7569 (tpp) cc_final: 0.7314 (mmm) REVERT: A 408 MET cc_start: 0.6133 (mmm) cc_final: 0.5733 (mmm) REVERT: A 485 MET cc_start: 0.4461 (ptt) cc_final: 0.4122 (ppp) REVERT: B 6 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.5818 (pp) REVERT: B 50 MET cc_start: 0.7529 (mtm) cc_final: 0.6949 (mtm) REVERT: C 22 TYR cc_start: 0.6471 (OUTLIER) cc_final: 0.5388 (t80) REVERT: C 207 MET cc_start: 0.8247 (mmm) cc_final: 0.7887 (mmm) REVERT: C 485 MET cc_start: 0.5723 (ppp) cc_final: 0.5319 (ppp) REVERT: D 15 MET cc_start: 0.8344 (ptm) cc_final: 0.7839 (ptp) REVERT: D 99 MET cc_start: 0.7134 (tpp) cc_final: 0.6934 (tpp) REVERT: D 408 MET cc_start: 0.6876 (mmt) cc_final: 0.6206 (mmm) REVERT: E 15 MET cc_start: 0.8345 (ptm) cc_final: 0.7996 (ptp) REVERT: E 196 MET cc_start: 0.8006 (ppp) cc_final: 0.7748 (ppp) REVERT: E 408 MET cc_start: 0.6674 (mmt) cc_final: 0.6250 (mmp) REVERT: E 450 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6851 (t70) REVERT: F 15 MET cc_start: 0.8471 (ptm) cc_final: 0.8140 (ptm) REVERT: F 50 MET cc_start: 0.7714 (mtm) cc_final: 0.7350 (mtm) REVERT: G 15 MET cc_start: 0.8531 (ptm) cc_final: 0.8266 (ptm) REVERT: G 22 TYR cc_start: 0.6337 (OUTLIER) cc_final: 0.5704 (t80) REVERT: H 15 MET cc_start: 0.8324 (ptm) cc_final: 0.7929 (ptm) REVERT: H 176 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6575 (mtm) REVERT: H 207 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7898 (mtm) REVERT: H 408 MET cc_start: 0.7166 (mmt) cc_final: 0.6962 (mmm) REVERT: I 22 TYR cc_start: 0.6948 (t80) cc_final: 0.6698 (t80) REVERT: I 24 MET cc_start: 0.7848 (ttm) cc_final: 0.7369 (ttm) REVERT: I 50 MET cc_start: 0.7763 (mtm) cc_final: 0.7291 (mtm) REVERT: I 128 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8960 (mt) REVERT: I 207 MET cc_start: 0.8022 (mmm) cc_final: 0.7688 (mmm) REVERT: I 485 MET cc_start: 0.5794 (ppp) cc_final: 0.5120 (ppp) REVERT: J 15 MET cc_start: 0.8534 (ptm) cc_final: 0.8113 (ptp) REVERT: J 99 MET cc_start: 0.6929 (tpp) cc_final: 0.6603 (tpp) REVERT: K 15 MET cc_start: 0.8457 (ptm) cc_final: 0.8083 (ptm) REVERT: K 22 TYR cc_start: 0.6358 (OUTLIER) cc_final: 0.5360 (t80) REVERT: K 485 MET cc_start: 0.6166 (ppp) cc_final: 0.5944 (ppp) REVERT: L 6 LEU cc_start: 0.6857 (mt) cc_final: 0.6109 (pp) REVERT: L 15 MET cc_start: 0.8470 (ptm) cc_final: 0.8112 (ptm) REVERT: L 72 MET cc_start: 0.6284 (mmm) cc_final: 0.5905 (mmm) REVERT: L 408 MET cc_start: 0.6911 (mmp) cc_final: 0.6639 (mmp) outliers start: 137 outliers final: 103 residues processed: 492 average time/residue: 0.5060 time to fit residues: 429.8177 Evaluate side-chains 499 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 388 time to evaluate : 5.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 207 MET Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 450 ASP Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP 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: 6.9990 chunk 167 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 352 optimal weight: 2.9990 chunk 378 optimal weight: 4.9990 chunk 274 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 436 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 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 5 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 GLN ** 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** ** 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** ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 46728 Z= 0.270 Angle : 0.666 13.340 62964 Z= 0.350 Chirality : 0.044 0.212 7188 Planarity : 0.004 0.049 8172 Dihedral : 5.147 29.448 6384 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.79 % Allowed : 10.21 % Favored : 87.00 % 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: -0.18 (0.12), residues: 5772 helix: 1.45 (0.09), residues: 3036 sheet: -1.66 (0.22), residues: 552 loop : -2.01 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 93 HIS 0.003 0.001 HIS F 354 PHE 0.024 0.002 PHE B 19 TYR 0.018 0.002 TYR I 351 ARG 0.011 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 393 time to evaluate : 5.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.9001 (mt) REVERT: A 207 MET cc_start: 0.7585 (tpp) cc_final: 0.7225 (mmm) REVERT: A 408 MET cc_start: 0.6225 (mmm) cc_final: 0.5821 (mmm) REVERT: A 485 MET cc_start: 0.4502 (OUTLIER) cc_final: 0.4115 (ptt) REVERT: B 6 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.5819 (pp) REVERT: B 50 MET cc_start: 0.7605 (mtm) cc_final: 0.7072 (mtm) REVERT: C 22 TYR cc_start: 0.6549 (OUTLIER) cc_final: 0.5409 (t80) REVERT: C 207 MET cc_start: 0.8221 (mmm) cc_final: 0.7889 (mmm) REVERT: C 485 MET cc_start: 0.5876 (ppp) cc_final: 0.5508 (ppp) REVERT: D 15 MET cc_start: 0.8346 (ptm) cc_final: 0.7844 (ptp) REVERT: D 99 MET cc_start: 0.7146 (tpp) cc_final: 0.6840 (tpp) REVERT: D 210 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8470 (mm) REVERT: E 15 MET cc_start: 0.8321 (ptm) cc_final: 0.7973 (ptp) REVERT: E 196 MET cc_start: 0.7993 (ppp) cc_final: 0.7687 (ppp) REVERT: E 450 ASP cc_start: 0.7283 (OUTLIER) cc_final: 0.6863 (t70) REVERT: F 15 MET cc_start: 0.8441 (ptm) cc_final: 0.8093 (ptm) REVERT: F 50 MET cc_start: 0.7723 (mtm) cc_final: 0.7382 (mtm) REVERT: F 128 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9124 (mt) REVERT: F 264 MET cc_start: 0.8290 (mmt) cc_final: 0.8074 (mmm) REVERT: F 408 MET cc_start: 0.6806 (mmt) cc_final: 0.6239 (mmm) REVERT: F 485 MET cc_start: 0.5868 (ppp) cc_final: 0.5654 (ppp) REVERT: G 6 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.5726 (pp) REVERT: G 15 MET cc_start: 0.8431 (ptm) cc_final: 0.8081 (ptm) REVERT: G 22 TYR cc_start: 0.6371 (OUTLIER) cc_final: 0.5637 (t80) REVERT: G 99 MET cc_start: 0.6438 (tpp) cc_final: 0.6218 (tpp) REVERT: H 15 MET cc_start: 0.8243 (ptm) cc_final: 0.7757 (ptm) REVERT: H 176 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6576 (mtm) REVERT: I 22 TYR cc_start: 0.6953 (t80) cc_final: 0.6558 (t80) REVERT: I 24 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7377 (ttm) REVERT: I 50 MET cc_start: 0.7735 (mtm) cc_final: 0.7250 (mtm) REVERT: I 128 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8953 (mt) REVERT: I 207 MET cc_start: 0.7946 (mmm) cc_final: 0.7643 (mmm) REVERT: I 485 MET cc_start: 0.5446 (ppp) cc_final: 0.4661 (ppp) REVERT: J 15 MET cc_start: 0.8487 (ptm) cc_final: 0.8070 (ptp) REVERT: J 99 MET cc_start: 0.6918 (tpp) cc_final: 0.6590 (tpp) REVERT: J 207 MET cc_start: 0.8139 (mtp) cc_final: 0.7924 (mmm) REVERT: J 320 MET cc_start: 0.7989 (tpp) cc_final: 0.7646 (tpp) REVERT: J 485 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.5491 (ppp) REVERT: K 15 MET cc_start: 0.8463 (ptm) cc_final: 0.8069 (ptm) REVERT: K 22 TYR cc_start: 0.6240 (OUTLIER) cc_final: 0.5262 (t80) REVERT: K 408 MET cc_start: 0.6911 (mmt) cc_final: 0.6418 (mmm) REVERT: K 485 MET cc_start: 0.6105 (ppp) cc_final: 0.5842 (ppp) REVERT: L 6 LEU cc_start: 0.6954 (mt) cc_final: 0.6260 (pp) REVERT: L 15 MET cc_start: 0.8470 (ptm) cc_final: 0.8095 (ptm) REVERT: L 72 MET cc_start: 0.6366 (mmm) cc_final: 0.6006 (mmm) REVERT: L 408 MET cc_start: 0.6907 (mmp) cc_final: 0.6646 (mmp) outliers start: 140 outliers final: 110 residues processed: 491 average time/residue: 0.5168 time to fit residues: 438.8923 Evaluate side-chains 512 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 388 time to evaluate : 5.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASN Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 207 MET Chi-restraints excluded: chain H residue 261 PHE Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 450 ASP Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain L residue 19 PHE Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 110 MET Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 505 optimal weight: 5.9990 chunk 531 optimal weight: 0.0370 chunk 485 optimal weight: 4.9990 chunk 517 optimal weight: 6.9990 chunk 311 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 406 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 467 optimal weight: 6.9990 chunk 489 optimal weight: 10.0000 chunk 515 optimal weight: 9.9990 overall best weight: 5.0066 ------------------------------------------------------------------------------- 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** ** A 355 GLN ** 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 5 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN ** 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 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 GLN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 167 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** ** 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 43 HIS ** K 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 355 GLN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 355 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 46728 Z= 0.287 Angle : 0.690 14.078 62964 Z= 0.362 Chirality : 0.045 0.219 7188 Planarity : 0.005 0.054 8172 Dihedral : 5.229 29.151 6384 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.83 % Allowed : 10.41 % Favored : 86.76 % 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: 1.42 (0.09), residues: 3036 sheet: -1.63 (0.22), residues: 552 loop : -2.00 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 94 HIS 0.004 0.001 HIS F 354 PHE 0.039 0.002 PHE K 19 TYR 0.019 0.002 TYR J 75 ARG 0.013 0.000 ARG F 306 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 390 time to evaluate : 5.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8988 (mt) REVERT: A 207 MET cc_start: 0.7573 (tpp) cc_final: 0.7218 (mmm) REVERT: A 408 MET cc_start: 0.6276 (mmm) cc_final: 0.5894 (mmm) REVERT: A 485 MET cc_start: 0.4629 (OUTLIER) cc_final: 0.4208 (ptt) REVERT: B 6 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.5965 (pp) REVERT: B 50 MET cc_start: 0.7601 (mtm) cc_final: 0.7041 (mtm) REVERT: B 323 MET cc_start: 0.6174 (tpp) cc_final: 0.5953 (tpp) REVERT: B 408 MET cc_start: 0.7049 (mmt) cc_final: 0.6568 (mmm) REVERT: C 22 TYR cc_start: 0.6457 (OUTLIER) cc_final: 0.5473 (t80) REVERT: C 207 MET cc_start: 0.8169 (mmm) cc_final: 0.7851 (mmm) REVERT: C 485 MET cc_start: 0.5839 (ppp) cc_final: 0.5490 (ppp) REVERT: D 15 MET cc_start: 0.8356 (ptm) cc_final: 0.7856 (ptp) REVERT: D 99 MET cc_start: 0.7127 (tpp) cc_final: 0.6818 (tpp) REVERT: D 207 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7731 (mmm) REVERT: E 15 MET cc_start: 0.8343 (ptm) cc_final: 0.7984 (ptp) REVERT: E 196 MET cc_start: 0.7935 (ppp) cc_final: 0.7650 (ppp) REVERT: E 408 MET cc_start: 0.6666 (mmt) cc_final: 0.6272 (mmp) REVERT: E 450 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6894 (t70) REVERT: F 6 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6545 (pt) REVERT: F 15 MET cc_start: 0.8462 (ptm) cc_final: 0.8088 (ptm) REVERT: F 50 MET cc_start: 0.7710 (mtm) cc_final: 0.7378 (mtm) REVERT: F 128 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.9133 (mt) REVERT: F 408 MET cc_start: 0.6850 (mmt) cc_final: 0.6540 (mmt) REVERT: G 6 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.5933 (pp) REVERT: G 15 MET cc_start: 0.8451 (ptm) cc_final: 0.8090 (ptm) REVERT: G 22 TYR cc_start: 0.6336 (OUTLIER) cc_final: 0.5717 (t80) REVERT: G 207 MET cc_start: 0.8442 (mmm) cc_final: 0.8039 (mmm) REVERT: H 15 MET cc_start: 0.8248 (ptm) cc_final: 0.7740 (ptm) REVERT: H 176 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6422 (mtm) REVERT: I 22 TYR cc_start: 0.6946 (t80) cc_final: 0.6587 (t80) REVERT: I 24 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7435 (ttm) REVERT: I 50 MET cc_start: 0.7726 (mtm) cc_final: 0.7250 (mtm) REVERT: I 128 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.9000 (mt) REVERT: I 207 MET cc_start: 0.7944 (mmm) cc_final: 0.7728 (mmm) REVERT: I 485 MET cc_start: 0.5360 (ppp) cc_final: 0.4610 (ppp) REVERT: J 15 MET cc_start: 0.8492 (ptm) cc_final: 0.8077 (ptp) REVERT: J 99 MET cc_start: 0.6947 (tpp) cc_final: 0.6652 (tpp) REVERT: J 207 MET cc_start: 0.8193 (mtp) cc_final: 0.7973 (mmm) REVERT: J 264 MET cc_start: 0.8435 (mmt) cc_final: 0.7978 (mmt) REVERT: J 320 MET cc_start: 0.7965 (tpp) cc_final: 0.7667 (tpp) REVERT: J 408 MET cc_start: 0.6937 (mmt) cc_final: 0.6265 (mmm) REVERT: J 485 MET cc_start: 0.5798 (OUTLIER) cc_final: 0.5457 (ppp) REVERT: K 15 MET cc_start: 0.8421 (ptm) cc_final: 0.8046 (ptm) REVERT: K 22 TYR cc_start: 0.6270 (OUTLIER) cc_final: 0.5346 (t80) REVERT: K 408 MET cc_start: 0.6963 (mmt) cc_final: 0.6574 (mmm) REVERT: L 6 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6366 (pp) REVERT: L 15 MET cc_start: 0.8480 (ptm) cc_final: 0.8091 (ptm) REVERT: L 72 MET cc_start: 0.6010 (mmm) cc_final: 0.5658 (mmm) REVERT: L 408 MET cc_start: 0.6907 (mmp) cc_final: 0.6653 (mmp) outliers start: 142 outliers final: 113 residues processed: 490 average time/residue: 0.5156 time to fit residues: 436.0486 Evaluate side-chains 516 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 387 time to evaluate : 5.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 450 ASP Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 5 ASN Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 188 THR Chi-restraints excluded: chain D residue 207 MET Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 20 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 338 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 450 ASP Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 207 MET Chi-restraints excluded: chain H residue 261 PHE Chi-restraints excluded: chain H residue 338 ILE Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain H residue 450 ASP Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 6 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 170 THR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 450 ASP Chi-restraints excluded: chain J residue 20 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 450 ASP Chi-restraints excluded: chain J residue 465 ILE Chi-restraints excluded: chain J residue 485 MET Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 22 TYR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain K residue 450 ASP Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 19 PHE Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 110 MET Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 348 LEU Chi-restraints excluded: chain L residue 422 LEU Chi-restraints excluded: chain L residue 450 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 0.9980 chunk 547 optimal weight: 0.0170 chunk 333 optimal weight: 8.9990 chunk 259 optimal weight: 0.4980 chunk 380 optimal weight: 8.9990 chunk 573 optimal weight: 0.6980 chunk 528 optimal weight: 8.9990 chunk 456 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 352 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- 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** ** A 375 HIS ** 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 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** ** 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 375 HIS ** 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 375 HIS ** 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** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 46728 Z= 0.156 Angle : 0.613 14.533 62964 Z= 0.312 Chirality : 0.043 0.218 7188 Planarity : 0.004 0.053 8172 Dihedral : 4.673 28.551 6384 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.28 % Allowed : 11.94 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.12), residues: 5772 helix: 1.87 (0.10), residues: 2988 sheet: -1.51 (0.22), residues: 552 loop : -1.89 (0.14), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 93 HIS 0.002 0.000 HIS A 228 PHE 0.014 0.001 PHE L 19 TYR 0.013 0.002 TYR K 263 ARG 0.013 0.001 ARG L 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11544 Ramachandran restraints generated. 5772 Oldfield, 0 Emsley, 5772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 461 time to evaluate : 5.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 MET cc_start: 0.8347 (mmt) cc_final: 0.8127 (mmt) REVERT: A 485 MET cc_start: 0.4441 (ptt) cc_final: 0.3938 (ptt) REVERT: B 6 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5570 (pp) REVERT: B 50 MET cc_start: 0.7461 (mtm) cc_final: 0.7091 (mtm) REVERT: B 408 MET cc_start: 0.6738 (mmt) cc_final: 0.6276 (mmm) REVERT: C 22 TYR cc_start: 0.6078 (OUTLIER) cc_final: 0.4972 (t80) REVERT: C 207 MET cc_start: 0.8136 (mmm) cc_final: 0.7711 (mmm) REVERT: C 408 MET cc_start: 0.6822 (mmt) cc_final: 0.6221 (mmm) REVERT: C 485 MET cc_start: 0.6015 (ppp) cc_final: 0.5607 (ppp) REVERT: D 15 MET cc_start: 0.8220 (ptm) cc_final: 0.7868 (ptm) REVERT: D 99 MET cc_start: 0.6699 (tpp) cc_final: 0.6424 (tpp) REVERT: E 15 MET cc_start: 0.8204 (ptm) cc_final: 0.7798 (ptp) REVERT: E 408 MET cc_start: 0.6441 (mmt) cc_final: 0.6196 (mmm) REVERT: F 15 MET cc_start: 0.8159 (ptm) cc_final: 0.7765 (ptm) REVERT: F 50 MET cc_start: 0.7802 (mtm) cc_final: 0.7296 (mtm) REVERT: F 207 MET cc_start: 0.8252 (mmm) cc_final: 0.8043 (mmm) REVERT: F 264 MET cc_start: 0.8126 (mmm) cc_final: 0.7730 (mmt) REVERT: G 22 TYR cc_start: 0.6316 (OUTLIER) cc_final: 0.5414 (t80) REVERT: G 50 MET cc_start: 0.8176 (mpp) cc_final: 0.7923 (mtm) REVERT: G 207 MET cc_start: 0.8423 (mmm) cc_final: 0.8086 (mmm) REVERT: G 408 MET cc_start: 0.6458 (mmt) cc_final: 0.5840 (mmm) REVERT: H 15 MET cc_start: 0.8016 (ptm) cc_final: 0.7668 (ptm) REVERT: H 264 MET cc_start: 0.8243 (mmt) cc_final: 0.7833 (mmt) REVERT: H 408 MET cc_start: 0.6247 (mmt) cc_final: 0.5441 (mmm) REVERT: I 24 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7331 (ttm) REVERT: I 50 MET cc_start: 0.7647 (mtm) cc_final: 0.6848 (mtm) REVERT: I 207 MET cc_start: 0.8080 (mmm) cc_final: 0.7678 (mmm) REVERT: I 264 MET cc_start: 0.7926 (mmm) cc_final: 0.7371 (mmt) REVERT: I 320 MET cc_start: 0.7930 (tpp) cc_final: 0.7716 (tpp) REVERT: I 408 MET cc_start: 0.6447 (mmt) cc_final: 0.5801 (mmm) REVERT: I 485 MET cc_start: 0.5484 (ppp) cc_final: 0.4835 (pmm) REVERT: J 15 MET cc_start: 0.8163 (ptm) cc_final: 0.7847 (ptp) REVERT: J 187 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7160 (pt0) REVERT: J 408 MET cc_start: 0.6506 (mmt) cc_final: 0.5771 (mmm) REVERT: K 15 MET cc_start: 0.8159 (ptm) cc_final: 0.7743 (ptm) REVERT: K 485 MET cc_start: 0.6096 (ppp) cc_final: 0.5736 (ppp) REVERT: L 6 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.5911 (pp) REVERT: L 15 MET cc_start: 0.8409 (ptm) cc_final: 0.8009 (ptm) REVERT: L 72 MET cc_start: 0.6344 (mmm) cc_final: 0.6003 (mmm) REVERT: L 342 LEU cc_start: 0.8580 (mm) cc_final: 0.8376 (mt) REVERT: L 408 MET cc_start: 0.6791 (mmp) cc_final: 0.6505 (mmp) outliers start: 64 outliers final: 43 residues processed: 502 average time/residue: 0.5327 time to fit residues: 456.1465 Evaluate side-chains 450 residues out of total 5016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 401 time to evaluate : 5.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain C residue 22 TYR Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 348 LEU Chi-restraints excluded: chain G residue 22 TYR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 348 LEU Chi-restraints excluded: chain H residue 24 MET Chi-restraints excluded: chain H residue 261 PHE Chi-restraints excluded: chain H residue 348 LEU Chi-restraints excluded: chain H residue 468 GLU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 96 TYR Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 348 LEU Chi-restraints excluded: chain I residue 469 LEU Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 110 MET Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 348 LEU Chi-restraints excluded: chain K residue 170 THR Chi-restraints excluded: chain K residue 348 LEU Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 110 MET Chi-restraints excluded: chain L residue 239 VAL Chi-restraints excluded: chain L residue 348 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 362 optimal weight: 0.0670 chunk 486 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 421 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 457 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 469 optimal weight: 6.9990 chunk 57 optimal weight: 0.0060 chunk 84 optimal weight: 4.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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** ** 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** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 HIS ** 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** ** D 375 HIS ** 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 375 HIS ** 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 375 HIS ** 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 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 375 HIS ** 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 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN ** 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 375 HIS ** 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 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.087794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.071323 restraints weight = 218662.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.072823 restraints weight = 146122.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.073861 restraints weight = 109681.150| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 46728 Z= 0.156 Angle : 0.633 13.700 62964 Z= 0.317 Chirality : 0.043 0.195 7188 Planarity : 0.004 0.058 8172 Dihedral : 4.563 28.028 6384 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.30 % Allowed : 12.72 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.12), residues: 5772 helix: 1.94 (0.10), residues: 3000 sheet: -1.43 (0.22), residues: 552 loop : -1.84 (0.14), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 93 HIS 0.006 0.001 HIS J 43 PHE 0.025 0.001 PHE K 19 TYR 0.013 0.001 TYR J 263 ARG 0.008 0.000 ARG C 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8922.93 seconds wall clock time: 162 minutes 38.57 seconds (9758.57 seconds total)