Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 07:29:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6v_21564/04_2023/6w6v_21564.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6v_21564/04_2023/6w6v_21564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6v_21564/04_2023/6w6v_21564.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6v_21564/04_2023/6w6v_21564.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6v_21564/04_2023/6w6v_21564.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6v_21564/04_2023/6w6v_21564.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.094 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: 5 Type Number sf(0) Gaussians P 295 5.49 5 S 90 5.16 5 C 14572 2.51 5 N 4418 2.21 5 O 5475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "B ASP 474": "OD1" <-> "OD2" Residue "B TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 549": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B ARG 676": "NH1" <-> "NH2" Residue "B PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 760": "NH1" <-> "NH2" Residue "B ARG 858": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "H ARG 7": "NH1" <-> "NH2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "I ARG 68": "NH1" <-> "NH2" Residue "I GLU 71": "OE1" <-> "OE2" Residue "I ARG 83": "NH1" <-> "NH2" Residue "I ASP 105": "OD1" <-> "OD2" Residue "I TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 178": "NH1" <-> "NH2" Residue "I ARG 182": "NH1" <-> "NH2" Residue "I GLU 200": "OE1" <-> "OE2" Residue "I ARG 220": "NH1" <-> "NH2" Residue "I ARG 237": "NH1" <-> "NH2" Residue "J ASP 16": "OD1" <-> "OD2" Residue "J ARG 67": "NH1" <-> "NH2" Residue "J TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 83": "NH1" <-> "NH2" Residue "J ASP 89": "OD1" <-> "OD2" Residue "J ASP 105": "OD1" <-> "OD2" Residue "J PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 178": "NH1" <-> "NH2" Residue "J ARG 182": "NH1" <-> "NH2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 24850 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 294, 6239 Classifications: {'RNA': 294} Modifications used: {'rna2p_pur': 24, 'rna2p_pyr': 21, 'rna3p_pur': 125, 'rna3p_pyr': 124} Link IDs: {'rna2p': 45, 'rna3p': 248} Chain breaks: 7 Conformer: "B" Number of residues, atoms: 294, 6239 Classifications: {'RNA': 294} Modifications used: {'rna2p_pur': 24, 'rna2p_pyr': 21, 'rna3p_pur': 125, 'rna3p_pyr': 124} Link IDs: {'rna2p': 45, 'rna3p': 248} Chain breaks: 7 bond proxies already assigned to first conformer: 6942 Chain: "B" Number of atoms: 6345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6345 Classifications: {'peptide': 780} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 743} Chain breaks: 3 Chain: "D" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1759 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 5, 'TRANS': 206} Chain: "E" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1335 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain: "F" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1280 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 154} Chain: "G" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1006 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain breaks: 1 Chain: "H" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1033 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain: "I" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1891 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "J" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2260 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain: "K" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 648 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "L" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1032 Classifications: {'peptide': 121} Link IDs: {'TRANS': 120} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" P A A A 113 " occ=0.50 ... (42 atoms not shown) pdb=" C4 B A A 113 " occ=0.50 Time building chain proxies: 15.82, per 1000 atoms: 0.64 Number of scatterers: 24850 At special positions: 0 Unit cell: (125.685, 156.94, 150.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 295 15.00 O 5475 8.00 N 4418 7.00 C 14572 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: 10.24 Conformation dependent library (CDL) restraints added in 2.7 seconds 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4390 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 15 sheets defined 36.9% alpha, 13.9% beta 78 base pairs and 137 stacking pairs defined. Time for finding SS restraints: 6.83 Creating SS restraints... Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.954A pdb=" N ALA B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 4.173A pdb=" N ARG B 97 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 122 removed outlier: 3.686A pdb=" N ARG B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 116 " --> pdb=" O MET B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 163 removed outlier: 4.021A pdb=" N LYS B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.567A pdb=" N LYS B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.622A pdb=" N HIS B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 318 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 374 through 383 removed outlier: 3.866A pdb=" N VAL B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 381 " --> pdb=" O GLN B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 422 through 432 Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.669A pdb=" N LEU B 456 " --> pdb=" O PRO B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 467 removed outlier: 3.823A pdb=" N GLN B 466 " --> pdb=" O ASN B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.503A pdb=" N HIS B 479 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 492 removed outlier: 3.769A pdb=" N VAL B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 509 through 519 Processing helix chain 'B' and resid 520 through 523 removed outlier: 4.090A pdb=" N ALA B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 523' Processing helix chain 'B' and resid 564 through 573 removed outlier: 3.659A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 571 " --> pdb=" O PRO B 567 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN B 573 " --> pdb=" O TRP B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 593 Processing helix chain 'B' and resid 605 through 614 removed outlier: 3.806A pdb=" N ILE B 610 " --> pdb=" O GLN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 625 removed outlier: 3.933A pdb=" N LYS B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 674 removed outlier: 3.898A pdb=" N LEU B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 714 Processing helix chain 'B' and resid 788 through 798 Processing helix chain 'B' and resid 816 through 818 No H-bonds generated for 'chain 'B' and resid 816 through 818' Processing helix chain 'B' and resid 844 through 848 removed outlier: 3.562A pdb=" N ILE B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 844 through 848' Processing helix chain 'D' and resid 77 through 105 removed outlier: 3.667A pdb=" N LYS D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU D 91 " --> pdb=" O ILE D 87 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 126 removed outlier: 3.574A pdb=" N HIS D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 130 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.037A pdb=" N ILE D 151 " --> pdb=" O TRP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.569A pdb=" N SER D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 278 Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.672A pdb=" N LEU E 32 " --> pdb=" O LYS E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.695A pdb=" N ILE E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.692A pdb=" N ASN E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 93 through 102 Processing helix chain 'E' and resid 123 through 142 removed outlier: 3.652A pdb=" N GLU E 127 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'E' and resid 155 through 162 removed outlier: 3.597A pdb=" N PHE E 159 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS E 160 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS E 161 " --> pdb=" O ASN E 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 30 removed outlier: 3.735A pdb=" N VAL F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 54 through 66 Processing helix chain 'F' and resid 87 through 102 removed outlier: 3.747A pdb=" N SER F 93 " --> pdb=" O GLN F 89 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY F 101 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR F 102 " --> pdb=" O PHE F 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 52 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'G' and resid 70 through 84 removed outlier: 3.929A pdb=" N LYS G 74 " --> pdb=" O LYS G 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 46 Processing helix chain 'H' and resid 47 through 51 Processing helix chain 'H' and resid 73 through 82 removed outlier: 3.513A pdb=" N SER H 79 " --> pdb=" O ASP H 75 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 Processing helix chain 'I' and resid 19 through 37 removed outlier: 4.196A pdb=" N VAL I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY I 37 " --> pdb=" O LEU I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 121 Processing helix chain 'I' and resid 142 through 152 removed outlier: 3.776A pdb=" N ILE I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 166 removed outlier: 3.851A pdb=" N ARG I 165 " --> pdb=" O GLY I 161 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP I 166 " --> pdb=" O TYR I 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 161 through 166' Processing helix chain 'I' and resid 166 through 184 removed outlier: 3.608A pdb=" N GLN I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG I 178 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER I 179 " --> pdb=" O SER I 175 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 213 Processing helix chain 'I' and resid 217 through 222 removed outlier: 4.001A pdb=" N SER I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 239 removed outlier: 3.587A pdb=" N LEU I 233 " --> pdb=" O ALA I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 243 removed outlier: 3.700A pdb=" N HIS I 243 " --> pdb=" O ASN I 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 240 through 243' Processing helix chain 'J' and resid 19 through 37 removed outlier: 3.540A pdb=" N VAL J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 removed outlier: 3.607A pdb=" N LEU J 60 " --> pdb=" O VAL J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 69 removed outlier: 3.517A pdb=" N PHE J 69 " --> pdb=" O ILE J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 77 Processing helix chain 'J' and resid 99 through 104 removed outlier: 3.589A pdb=" N ALA J 103 " --> pdb=" O LYS J 99 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE J 104 " --> pdb=" O ILE J 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 99 through 104' Processing helix chain 'J' and resid 113 through 120 Processing helix chain 'J' and resid 146 through 151 removed outlier: 4.140A pdb=" N ASN J 151 " --> pdb=" O CYS J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.827A pdb=" N LEU J 164 " --> pdb=" O GLY J 161 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG J 165 " --> pdb=" O TYR J 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 161 through 165' Processing helix chain 'J' and resid 167 through 184 removed outlier: 4.361A pdb=" N ARG J 171 " --> pdb=" O VAL J 167 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 201 Processing helix chain 'J' and resid 203 through 206 Processing helix chain 'J' and resid 207 through 213 removed outlier: 3.770A pdb=" N ASN J 213 " --> pdb=" O SER J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 225 removed outlier: 4.172A pdb=" N MET J 225 " --> pdb=" O CYS J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 238 Processing helix chain 'K' and resid 8 through 23 removed outlier: 4.173A pdb=" N ARG K 12 " --> pdb=" O LYS K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 46 Processing helix chain 'L' and resid 7 through 25 removed outlier: 4.378A pdb=" N GLN L 13 " --> pdb=" O ARG L 9 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG L 16 " --> pdb=" O GLU L 12 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN L 25 " --> pdb=" O LEU L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.862A pdb=" N ARG L 30 " --> pdb=" O ASN L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 50 removed outlier: 4.921A pdb=" N GLU L 40 " --> pdb=" O GLY L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 76 removed outlier: 3.824A pdb=" N ARG L 72 " --> pdb=" O LYS L 69 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG L 76 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 89 Processing helix chain 'L' and resid 90 through 96 removed outlier: 3.661A pdb=" N GLY L 96 " --> pdb=" O VAL L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 122 removed outlier: 4.048A pdb=" N ILE L 122 " --> pdb=" O ARG L 118 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 251 through 252 removed outlier: 6.964A pdb=" N HIS B 251 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 446 through 450 removed outlier: 6.334A pdb=" N ALA B 285 " --> pdb=" O TYR B 579 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 334 through 338 removed outlier: 3.519A pdb=" N PHE B 334 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 358 " --> pdb=" O PHE B 334 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 336 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS B 356 " --> pdb=" O GLY B 336 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 354 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 297 " --> pdb=" O GLN B 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 762 through 769 removed outlier: 5.478A pdb=" N GLY B 836 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE B 841 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE B 824 " --> pdb=" O PHE B 841 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP B 843 " --> pdb=" O GLY B 822 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY B 822 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 820 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN B 783 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 219 through 223 removed outlier: 7.295A pdb=" N ILE D 209 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS D 187 " --> pdb=" O VAL D 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 219 through 223 removed outlier: 7.295A pdb=" N ILE D 209 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS D 187 " --> pdb=" O VAL D 229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 73 through 77 removed outlier: 6.034A pdb=" N LEU E 74 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ARG E 87 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TYR E 76 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS E 118 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU E 12 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE E 14 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL E 114 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AA9, first strand: chain 'F' and resid 47 through 48 removed outlier: 6.947A pdb=" N HIS F 47 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N TYR F 84 " --> pdb=" O HIS F 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 16 through 17 removed outlier: 3.967A pdb=" N THR G 16 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU G 102 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 55 through 57 removed outlier: 3.922A pdb=" N ILE H 67 " --> pdb=" O PHE H 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 3 through 8 removed outlier: 4.471A pdb=" N VAL I 3 " --> pdb=" O HIS I 40 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA I 42 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU I 5 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN I 44 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL I 7 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE I 41 " --> pdb=" O TYR I 81 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ARG I 83 " --> pdb=" O ILE I 41 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE I 43 " --> pdb=" O ARG I 83 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR I 85 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 10.157A pdb=" N ILE I 106 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N SER I 82 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N ALA I 108 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE I 84 " --> pdb=" O ALA I 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 156 through 158 removed outlier: 6.267A pdb=" N LEU I 156 " --> pdb=" O VAL I 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'J' and resid 3 through 4 removed outlier: 7.193A pdb=" N ASP J 4 " --> pdb=" O ALA J 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 46 through 48 removed outlier: 3.864A pdb=" N LEU J 128 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU J 157 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU J 156 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N GLY J 192 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE J 158 " --> pdb=" O GLY J 192 " (cutoff:3.500A) 613 hydrogen bonds defined for protein. 1701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 197 hydrogen bonds 366 hydrogen bond angles 0 basepair planarities 78 basepair parallelities 137 stacking parallelities Total time for adding SS restraints: 9.35 Time building geometry restraints manager: 10.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5800 1.33 - 1.45: 6533 1.45 - 1.57: 12859 1.57 - 1.69: 584 1.69 - 1.81: 139 Bond restraints: 25915 Sorted by residual: bond pdb=" C PRO B 171 " pdb=" N PRO B 172 " ideal model delta sigma weight residual 1.334 1.375 -0.041 2.34e-02 1.83e+03 3.07e+00 bond pdb=" CB PRO I 54 " pdb=" CG PRO I 54 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.84e+00 bond pdb=" CG1 ILE J 181 " pdb=" CD1 ILE J 181 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.33e+00 bond pdb=" CG PRO I 54 " pdb=" CD PRO I 54 " ideal model delta sigma weight residual 1.503 1.540 -0.037 3.40e-02 8.65e+02 1.22e+00 bond pdb=" CG LEU G 66 " pdb=" CD2 LEU G 66 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.21e+00 ... (remaining 25910 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.18: 1554 105.18 - 112.39: 13867 112.39 - 119.60: 8650 119.60 - 126.81: 11344 126.81 - 134.03: 946 Bond angle restraints: 36361 Sorted by residual: angle pdb=" C TYR K 68 " pdb=" N VAL K 69 " pdb=" CA VAL K 69 " ideal model delta sigma weight residual 123.25 117.24 6.01 1.10e+00 8.26e-01 2.99e+01 angle pdb=" CA ARG B 626 " pdb=" CB ARG B 626 " pdb=" CG ARG B 626 " ideal model delta sigma weight residual 114.10 124.73 -10.63 2.00e+00 2.50e-01 2.82e+01 angle pdb=" CA LEU G 66 " pdb=" CB LEU G 66 " pdb=" CG LEU G 66 " ideal model delta sigma weight residual 116.30 129.70 -13.40 3.50e+00 8.16e-02 1.47e+01 angle pdb=" CA PRO I 54 " pdb=" N PRO I 54 " pdb=" CD PRO I 54 " ideal model delta sigma weight residual 112.00 106.75 5.25 1.40e+00 5.10e-01 1.41e+01 angle pdb=" CA GLY I 192 " pdb=" C GLY I 192 " pdb=" N SER I 193 " ideal model delta sigma weight residual 114.65 117.93 -3.28 9.20e-01 1.18e+00 1.27e+01 ... (remaining 36356 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.37: 13998 22.37 - 44.75: 973 44.75 - 67.12: 147 67.12 - 89.49: 19 89.49 - 111.87: 5 Dihedral angle restraints: 15142 sinusoidal: 8381 harmonic: 6761 Sorted by residual: dihedral pdb=" CA VAL D 140 " pdb=" C VAL D 140 " pdb=" N PRO D 141 " pdb=" CA PRO D 141 " ideal model delta harmonic sigma weight residual -180.00 -151.02 -28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA PHE D 207 " pdb=" C PHE D 207 " pdb=" N PHE D 208 " pdb=" CA PHE D 208 " ideal model delta harmonic sigma weight residual 180.00 155.93 24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA ARG D 260 " pdb=" C ARG D 260 " pdb=" N ALA D 261 " pdb=" CA ALA D 261 " ideal model delta harmonic sigma weight residual -180.00 -159.00 -21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 15139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3358 0.044 - 0.088: 764 0.088 - 0.132: 192 0.132 - 0.176: 26 0.176 - 0.220: 5 Chirality restraints: 4345 Sorted by residual: chirality pdb=" CG LEU G 66 " pdb=" CB LEU G 66 " pdb=" CD1 LEU G 66 " pdb=" CD2 LEU G 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE B 700 " pdb=" CA ILE B 700 " pdb=" CG1 ILE B 700 " pdb=" CG2 ILE B 700 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C1' A A 86 " pdb=" O4' A A 86 " pdb=" C2' A A 86 " pdb=" N9 A A 86 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 4342 not shown) Planarity restraints: 3525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE I 53 " -0.066 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO I 54 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO I 54 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO I 54 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 140 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO D 141 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 560 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO B 561 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 561 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 561 " -0.031 5.00e-02 4.00e+02 ... (remaining 3522 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 549 2.65 - 3.22: 21917 3.22 - 3.78: 36703 3.78 - 4.34: 50494 4.34 - 4.90: 78226 Nonbonded interactions: 187889 Sorted by model distance: nonbonded pdb=" OG SER K 33 " pdb=" O VAL K 69 " model vdw 2.092 2.440 nonbonded pdb=" OG1 THR B 242 " pdb=" OD2 ASP B 289 " model vdw 2.104 2.440 nonbonded pdb=" O ASP H 75 " pdb=" OG SER H 79 " model vdw 2.145 2.440 nonbonded pdb=" O GLY I 206 " pdb=" OG SER I 209 " model vdw 2.186 2.440 nonbonded pdb=" OE1 GLU H 54 " pdb=" OG SER I 179 " model vdw 2.204 2.440 ... (remaining 187884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 30.410 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 68.240 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.004 0.084 25915 Z= 0.247 Angle : 0.633 13.397 36361 Z= 0.350 Chirality : 0.041 0.220 4345 Planarity : 0.004 0.097 3525 Dihedral : 14.191 111.867 10752 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.94 % Favored : 89.06 % Rotamer Outliers : 0.05 % 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: -2.45 (0.17), residues: 2276 helix: -0.56 (0.20), residues: 725 sheet: -0.45 (0.28), residues: 356 loop : -2.79 (0.16), residues: 1195 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 383 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 384 average time/residue: 1.3886 time to fit residues: 613.2267 Evaluate side-chains 269 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 2.247 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 3.0595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.1980 chunk 103 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 148 optimal weight: 0.1980 chunk 231 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 168 ASN H 36 GLN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN J 240 ASN J 264 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 25915 Z= 0.195 Angle : 0.594 12.461 36361 Z= 0.306 Chirality : 0.040 0.173 4345 Planarity : 0.004 0.063 3525 Dihedral : 11.960 111.178 6038 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer Outliers : 2.77 % 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: -2.06 (0.17), residues: 2276 helix: -0.02 (0.20), residues: 728 sheet: -0.24 (0.28), residues: 344 loop : -2.70 (0.16), residues: 1204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 305 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 21 residues processed: 327 average time/residue: 1.2900 time to fit residues: 490.0253 Evaluate side-chains 280 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 259 time to evaluate : 2.617 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 11 residues processed: 12 average time/residue: 0.4647 time to fit residues: 11.4339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 192 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 231 optimal weight: 0.6980 chunk 250 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 612 ASN E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN J 123 ASN J 168 GLN L 75 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 25915 Z= 0.198 Angle : 0.572 13.262 36361 Z= 0.293 Chirality : 0.039 0.154 4345 Planarity : 0.004 0.060 3525 Dihedral : 11.849 110.109 6038 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer Outliers : 2.72 % 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: -1.87 (0.17), residues: 2276 helix: 0.23 (0.21), residues: 724 sheet: -0.07 (0.28), residues: 352 loop : -2.68 (0.16), residues: 1200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 283 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 28 residues processed: 311 average time/residue: 1.3610 time to fit residues: 491.8580 Evaluate side-chains 287 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 259 time to evaluate : 2.553 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 12 residues processed: 16 average time/residue: 0.4534 time to fit residues: 13.6767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 229 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 246 optimal weight: 0.1980 chunk 121 optimal weight: 0.9980 chunk 220 optimal weight: 8.9990 chunk 66 optimal weight: 0.4980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 ASN L 71 HIS L 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.093 25915 Z= 0.161 Angle : 0.547 10.053 36361 Z= 0.279 Chirality : 0.038 0.174 4345 Planarity : 0.004 0.057 3525 Dihedral : 11.718 111.098 6038 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer Outliers : 2.82 % 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: -1.63 (0.18), residues: 2276 helix: 0.46 (0.21), residues: 722 sheet: 0.15 (0.29), residues: 345 loop : -2.57 (0.16), residues: 1209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 285 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 29 residues processed: 318 average time/residue: 1.2680 time to fit residues: 470.4739 Evaluate side-chains 285 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 256 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 14 residues processed: 15 average time/residue: 0.5247 time to fit residues: 14.0532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 205 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN H 36 GLN J 123 ASN L 71 HIS L 75 GLN L 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 25915 Z= 0.250 Angle : 0.601 10.414 36361 Z= 0.307 Chirality : 0.040 0.174 4345 Planarity : 0.004 0.059 3525 Dihedral : 11.835 109.529 6038 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer Outliers : 3.44 % 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: -1.73 (0.18), residues: 2276 helix: 0.31 (0.20), residues: 736 sheet: 0.00 (0.28), residues: 362 loop : -2.62 (0.17), residues: 1178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 264 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 32 residues processed: 306 average time/residue: 1.2634 time to fit residues: 453.4757 Evaluate side-chains 279 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 247 time to evaluate : 2.232 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 20 residues processed: 12 average time/residue: 0.4834 time to fit residues: 11.4640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 144 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 114 optimal weight: 0.0870 chunk 20 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 ASN L 71 HIS L 75 GLN L 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 25915 Z= 0.162 Angle : 0.555 10.048 36361 Z= 0.283 Chirality : 0.038 0.169 4345 Planarity : 0.004 0.057 3525 Dihedral : 11.711 110.974 6038 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer Outliers : 2.86 % 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: -1.59 (0.18), residues: 2276 helix: 0.41 (0.21), residues: 741 sheet: 0.14 (0.28), residues: 362 loop : -2.55 (0.17), residues: 1173 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 270 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 32 residues processed: 310 average time/residue: 1.3245 time to fit residues: 480.5706 Evaluate side-chains 285 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 253 time to evaluate : 2.320 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 22 residues processed: 10 average time/residue: 0.5863 time to fit residues: 11.2449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 237 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 ASN L 71 HIS L 75 GLN L 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 25915 Z= 0.253 Angle : 0.610 13.577 36361 Z= 0.310 Chirality : 0.040 0.164 4345 Planarity : 0.004 0.058 3525 Dihedral : 11.818 109.399 6038 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer Outliers : 3.20 % 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: -1.71 (0.18), residues: 2276 helix: 0.27 (0.20), residues: 750 sheet: 0.05 (0.28), residues: 362 loop : -2.60 (0.17), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 246 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 40 residues processed: 289 average time/residue: 1.3086 time to fit residues: 444.1222 Evaluate side-chains 285 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 245 time to evaluate : 2.270 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 25 residues processed: 15 average time/residue: 0.4783 time to fit residues: 13.4906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 74 optimal weight: 0.0770 chunk 48 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 193 optimal weight: 0.2980 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN J 123 ASN L 75 GLN L 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.054 25915 Z= 0.159 Angle : 0.563 11.880 36361 Z= 0.286 Chirality : 0.038 0.173 4345 Planarity : 0.004 0.056 3525 Dihedral : 11.660 110.892 6038 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer Outliers : 2.15 % 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: -1.49 (0.18), residues: 2276 helix: 0.42 (0.21), residues: 750 sheet: 0.26 (0.28), residues: 362 loop : -2.49 (0.17), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 260 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 30 residues processed: 295 average time/residue: 1.2961 time to fit residues: 447.8716 Evaluate side-chains 278 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 248 time to evaluate : 2.331 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 26 residues processed: 4 average time/residue: 0.7479 time to fit residues: 6.9919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 223 optimal weight: 0.4980 chunk 235 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 216 optimal weight: 8.9990 chunk 228 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 526 ASN E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 ASN H 128 GLN J 123 ASN J 235 ASN K 81 ASN L 71 HIS L 75 GLN L 81 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 25915 Z= 0.154 Angle : 0.564 11.155 36361 Z= 0.285 Chirality : 0.037 0.168 4345 Planarity : 0.004 0.054 3525 Dihedral : 11.559 110.590 6038 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer Outliers : 2.00 % 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: -1.37 (0.18), residues: 2276 helix: 0.51 (0.21), residues: 746 sheet: 0.36 (0.28), residues: 357 loop : -2.39 (0.17), residues: 1173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 261 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 30 residues processed: 289 average time/residue: 1.3319 time to fit residues: 451.8212 Evaluate side-chains 277 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 247 time to evaluate : 2.254 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 22 residues processed: 8 average time/residue: 0.4807 time to fit residues: 8.6702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 150 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 254 optimal weight: 0.6980 chunk 233 optimal weight: 0.7980 chunk 202 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN J 123 ASN K 63 HIS L 71 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 25915 Z= 0.293 Angle : 0.647 11.162 36361 Z= 0.328 Chirality : 0.041 0.173 4345 Planarity : 0.004 0.061 3525 Dihedral : 11.780 109.514 6038 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer Outliers : 1.91 % 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: -1.62 (0.18), residues: 2276 helix: 0.28 (0.20), residues: 744 sheet: 0.14 (0.28), residues: 366 loop : -2.52 (0.17), residues: 1166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 251 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 28 residues processed: 277 average time/residue: 1.3313 time to fit residues: 431.3005 Evaluate side-chains 271 residues out of total 2095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 243 time to evaluate : 2.477 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 21 residues processed: 8 average time/residue: 0.5255 time to fit residues: 9.0651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 160 optimal weight: 0.7980 chunk 215 optimal weight: 0.0770 chunk 61 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 202 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 0.3980 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** F 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 ASN H 128 GLN J 123 ASN L 71 HIS L 75 GLN L 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.138545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.104909 restraints weight = 76188.486| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.86 r_work: 0.3252 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 25915 Z= 0.156 Angle : 0.579 11.451 36361 Z= 0.293 Chirality : 0.038 0.188 4345 Planarity : 0.004 0.053 3525 Dihedral : 11.593 111.111 6038 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer Outliers : 1.58 % 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: -1.36 (0.18), residues: 2276 helix: 0.51 (0.21), residues: 741 sheet: 0.32 (0.28), residues: 363 loop : -2.36 (0.17), residues: 1172 =============================================================================== Job complete usr+sys time: 8391.63 seconds wall clock time: 150 minutes 46.37 seconds (9046.37 seconds total)