Starting phenix.real_space_refine on Sat Jul 20 02:36:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl0_36385/07_2024/8jl0_36385.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl0_36385/07_2024/8jl0_36385.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl0_36385/07_2024/8jl0_36385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl0_36385/07_2024/8jl0_36385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl0_36385/07_2024/8jl0_36385.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl0_36385/07_2024/8jl0_36385.cif" } resolution = 3.1 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= 0.002 sd= 0.033 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 46 5.49 5 S 33 5.16 5 C 5757 2.51 5 N 1583 2.21 5 O 1825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9244 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4572 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3712 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 440} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 450 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "C" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 466 Classifications: {'RNA': 22} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna2p': 2, 'rna3p': 19} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.48, per 1000 atoms: 0.70 Number of scatterers: 9244 At special positions: 0 Unit cell: (84.84, 115.08, 112.56, 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 33 16.00 P 46 15.00 O 1825 8.00 N 1583 7.00 C 5757 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: 3.66 Conformation dependent library (CDL) restraints added in 1.6 seconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 9 sheets defined 41.2% alpha, 17.9% beta 18 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 removed outlier: 3.816A pdb=" N GLN A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR A 13 " --> pdb=" O PHE A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 31 removed outlier: 4.281A pdb=" N SER A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 67 through 79 Processing helix chain 'A' and resid 87 through 98 removed outlier: 3.515A pdb=" N PHE A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 169 through 176 Processing helix chain 'A' and resid 200 through 219 removed outlier: 3.712A pdb=" N ASN A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 213 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.518A pdb=" N LYS A 260 " --> pdb=" O SER A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 Processing helix chain 'A' and resid 286 through 297 removed outlier: 3.851A pdb=" N GLN A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.528A pdb=" N ALA A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 removed outlier: 3.607A pdb=" N LYS A 366 " --> pdb=" O ARG A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.804A pdb=" N LYS A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 513 through 519 removed outlier: 3.575A pdb=" N ARG A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLU A 518 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 532 through 549 Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 39 through 43 removed outlier: 3.506A pdb=" N CYS B 43 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 60 through 71 removed outlier: 3.762A pdb=" N LEU B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 109 through 119 removed outlier: 4.128A pdb=" N HIS B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLY B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.950A pdb=" N GLU B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 192 through 209 removed outlier: 3.802A pdb=" N VAL B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 202 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 295 Processing helix chain 'B' and resid 312 through 321 removed outlier: 3.615A pdb=" N GLN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 removed outlier: 4.206A pdb=" N THR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 458 removed outlier: 4.069A pdb=" N GLN B 458 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 162 removed outlier: 7.227A pdb=" N MET A 20 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N PHE A 139 " --> pdb=" O MET A 20 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TRP A 22 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 221 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR A 254 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 223 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 355 through 356 removed outlier: 3.537A pdb=" N GLY A 582 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER A 580 " --> pdb=" O PRO A 329 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE A 579 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA B 10 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 581 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER B 12 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 12.386A pdb=" N LEU B 8 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N THR B 370 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA B 10 " --> pdb=" O PRO B 368 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 303 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL B 332 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE B 305 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE B 334 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS B 307 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA B 223 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS B 306 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 225 " --> pdb=" O HIS B 306 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY B 226 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 246 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER B 228 " --> pdb=" O CYS B 244 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 245 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 258 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 257 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.571A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS A 444 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 438 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.571A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 371 through 374 removed outlier: 4.932A pdb=" N VAL A 378 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 343 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 404 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 398 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 561 Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.511A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N CYS B 107 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N TYR B 54 " --> pdb=" O CYS B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.511A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ARG B 51 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU B 147 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA B 53 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N TYR B 149 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU B 55 " --> pdb=" O TYR B 149 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1410 1.31 - 1.43: 2851 1.43 - 1.56: 5155 1.56 - 1.69: 94 1.69 - 1.81: 51 Bond restraints: 9561 Sorted by residual: bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.247 0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" C4B NAD A 601 " pdb=" O4B NAD A 601 " ideal model delta sigma weight residual 1.433 1.678 -0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C3B NAD A 601 " pdb=" C4B NAD A 601 " ideal model delta sigma weight residual 1.523 1.280 0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C4D NAD A 601 " pdb=" O4D NAD A 601 " ideal model delta sigma weight residual 1.445 1.268 0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" C7N NAD A 601 " pdb=" N7N NAD A 601 " ideal model delta sigma weight residual 1.328 1.473 -0.145 2.00e-02 2.50e+03 5.24e+01 ... (remaining 9556 not shown) Histogram of bond angle deviations from ideal: 98.91 - 106.26: 498 106.26 - 113.61: 5229 113.61 - 120.95: 4543 120.95 - 128.30: 2782 128.30 - 135.65: 116 Bond angle restraints: 13168 Sorted by residual: angle pdb=" N PRO A 329 " pdb=" CA PRO A 329 " pdb=" C PRO A 329 " ideal model delta sigma weight residual 112.47 100.45 12.02 2.06e+00 2.36e-01 3.41e+01 angle pdb=" C3' A C 1 " pdb=" O3' A C 1 " pdb=" P U C 2 " ideal model delta sigma weight residual 120.20 113.69 6.51 1.50e+00 4.44e-01 1.89e+01 angle pdb=" O1A NAD A 601 " pdb=" PA NAD A 601 " pdb=" O2A NAD A 601 " ideal model delta sigma weight residual 122.64 109.73 12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" N THR A 176 " pdb=" CA THR A 176 " pdb=" C THR A 176 " ideal model delta sigma weight residual 113.20 108.19 5.01 1.21e+00 6.83e-01 1.72e+01 angle pdb=" CA SER A 327 " pdb=" C SER A 327 " pdb=" O SER A 327 " ideal model delta sigma weight residual 121.87 117.38 4.49 1.10e+00 8.26e-01 1.67e+01 ... (remaining 13163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.70: 5099 27.70 - 55.41: 521 55.41 - 83.11: 87 83.11 - 110.81: 5 110.81 - 138.51: 2 Dihedral angle restraints: 5714 sinusoidal: 2674 harmonic: 3040 Sorted by residual: dihedral pdb=" O4' C C 17 " pdb=" C1' C C 17 " pdb=" N1 C C 17 " pdb=" C2 C C 17 " ideal model delta sinusoidal sigma weight residual -160.00 -21.49 -138.51 1 1.50e+01 4.44e-03 7.46e+01 dihedral pdb=" CA LYS A 260 " pdb=" C LYS A 260 " pdb=" N SER A 261 " pdb=" CA SER A 261 " ideal model delta harmonic sigma weight residual -180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" C4' DC D 2 " pdb=" C3' DC D 2 " pdb=" O3' DC D 2 " pdb=" P DG D 3 " ideal model delta sinusoidal sigma weight residual -140.00 -7.37 -132.63 1 3.50e+01 8.16e-04 1.31e+01 ... (remaining 5711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1401 0.109 - 0.217: 58 0.217 - 0.326: 2 0.326 - 0.434: 2 0.434 - 0.543: 1 Chirality restraints: 1464 Sorted by residual: chirality pdb=" P A C 1 " pdb=" OP1 A C 1 " pdb=" OP2 A C 1 " pdb=" O5' A C 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" P U C 2 " pdb=" OP1 U C 2 " pdb=" OP2 U C 2 " pdb=" O5' U C 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.79 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" C3D NAD A 601 " pdb=" C2D NAD A 601 " pdb=" C4D NAD A 601 " pdb=" O3D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 1461 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 344 " 0.444 9.50e-02 1.11e+02 1.99e-01 2.43e+01 pdb=" NE ARG A 344 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG A 344 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 344 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 344 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 414 " 0.016 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C SER A 414 " -0.052 2.00e-02 2.50e+03 pdb=" O SER A 414 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 415 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 4 " -0.033 2.00e-02 2.50e+03 1.48e-02 6.04e+00 pdb=" N9 A C 4 " 0.035 2.00e-02 2.50e+03 pdb=" C8 A C 4 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A C 4 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A C 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A C 4 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A C 4 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A C 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A C 4 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A C 4 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A C 4 " 0.003 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1543 2.77 - 3.30: 8321 3.30 - 3.83: 15661 3.83 - 4.37: 18393 4.37 - 4.90: 30818 Nonbonded interactions: 74736 Sorted by model distance: nonbonded pdb=" OD1 ASN B 435 " pdb=" OG1 THR B 437 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR A 333 " pdb=" O ALA A 578 " model vdw 2.237 2.440 nonbonded pdb=" O ARG A 440 " pdb=" OG1 THR A 443 " model vdw 2.246 2.440 nonbonded pdb=" O2D NAD A 601 " pdb=" O3D NAD A 601 " model vdw 2.257 2.432 nonbonded pdb=" OD1 ASN B 436 " pdb=" O2' A C 3 " model vdw 2.273 2.440 ... (remaining 74731 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 32.740 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 0.008 0.284 9561 Z= 0.457 Angle : 0.728 12.913 13168 Z= 0.418 Chirality : 0.051 0.543 1464 Planarity : 0.006 0.199 1526 Dihedral : 20.611 138.513 3760 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.30 % Favored : 91.31 % Rotamer: Outliers : 0.79 % Allowed : 29.73 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.51 (0.25), residues: 1036 helix: 0.82 (0.28), residues: 358 sheet: -1.02 (0.37), residues: 199 loop : -2.50 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 377 HIS 0.006 0.001 HIS A 441 PHE 0.015 0.001 PHE A 91 TYR 0.015 0.002 TYR B 341 ARG 0.010 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 0.983 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 98 average time/residue: 0.2579 time to fit residues: 33.9657 Evaluate side-chains 89 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 415 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9561 Z= 0.167 Angle : 0.525 7.121 13168 Z= 0.283 Chirality : 0.040 0.207 1464 Planarity : 0.004 0.027 1526 Dihedral : 17.127 135.824 1788 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.01 % Favored : 91.80 % Rotamer: Outliers : 3.04 % Allowed : 29.62 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.09 (0.26), residues: 1036 helix: 1.19 (0.28), residues: 378 sheet: -0.78 (0.38), residues: 186 loop : -2.39 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 377 HIS 0.005 0.001 HIS A 441 PHE 0.012 0.001 PHE A 80 TYR 0.016 0.001 TYR A 74 ARG 0.007 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 0.981 Fit side-chains REVERT: A 260 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7788 (mmtp) REVERT: A 313 ARG cc_start: 0.6381 (tpt90) cc_final: 0.6166 (tpt170) REVERT: A 426 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7904 (mp) REVERT: B 149 TYR cc_start: 0.8334 (t80) cc_final: 0.8105 (t80) REVERT: B 221 ASP cc_start: 0.7436 (p0) cc_final: 0.7193 (p0) outliers start: 27 outliers final: 9 residues processed: 117 average time/residue: 0.2389 time to fit residues: 38.2735 Evaluate side-chains 98 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 401 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 80 optimal weight: 0.0270 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN A 204 ASN A 245 ASN A 441 HIS B 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9561 Z= 0.152 Angle : 0.499 6.854 13168 Z= 0.270 Chirality : 0.040 0.188 1464 Planarity : 0.004 0.028 1526 Dihedral : 16.966 134.481 1787 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.24 % Favored : 92.57 % Rotamer: Outliers : 4.84 % Allowed : 27.93 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.89 (0.26), residues: 1036 helix: 1.38 (0.28), residues: 379 sheet: -0.60 (0.39), residues: 186 loop : -2.34 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 377 HIS 0.005 0.001 HIS A 441 PHE 0.010 0.001 PHE A 80 TYR 0.012 0.001 TYR A 74 ARG 0.007 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 94 time to evaluate : 0.991 Fit side-chains REVERT: A 260 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7776 (mmtp) REVERT: B 221 ASP cc_start: 0.7454 (p0) cc_final: 0.7161 (p0) outliers start: 43 outliers final: 23 residues processed: 131 average time/residue: 0.2262 time to fit residues: 41.0051 Evaluate side-chains 110 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 426 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 0.0670 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9561 Z= 0.166 Angle : 0.506 7.519 13168 Z= 0.271 Chirality : 0.040 0.178 1464 Planarity : 0.004 0.031 1526 Dihedral : 16.898 135.262 1787 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.82 % Favored : 91.99 % Rotamer: Outliers : 4.28 % Allowed : 28.38 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.82 (0.26), residues: 1036 helix: 1.41 (0.28), residues: 379 sheet: -0.50 (0.39), residues: 187 loop : -2.32 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 377 HIS 0.003 0.001 HIS B 29 PHE 0.013 0.001 PHE A 91 TYR 0.015 0.001 TYR A 74 ARG 0.007 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 92 time to evaluate : 0.911 Fit side-chains REVERT: A 46 HIS cc_start: 0.5899 (OUTLIER) cc_final: 0.5084 (t70) REVERT: A 260 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7811 (mmtp) REVERT: A 572 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: B 221 ASP cc_start: 0.7502 (p0) cc_final: 0.7202 (p0) outliers start: 38 outliers final: 22 residues processed: 122 average time/residue: 0.2316 time to fit residues: 38.3609 Evaluate side-chains 110 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 401 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 77 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 92 optimal weight: 0.0370 chunk 26 optimal weight: 9.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9561 Z= 0.202 Angle : 0.527 7.064 13168 Z= 0.282 Chirality : 0.041 0.182 1464 Planarity : 0.004 0.036 1526 Dihedral : 16.913 137.362 1787 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.01 % Favored : 91.80 % Rotamer: Outliers : 4.84 % Allowed : 27.70 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.84 (0.26), residues: 1036 helix: 1.35 (0.28), residues: 378 sheet: -0.49 (0.39), residues: 187 loop : -2.29 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 377 HIS 0.003 0.001 HIS B 29 PHE 0.011 0.001 PHE A 328 TYR 0.015 0.001 TYR A 74 ARG 0.007 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 88 time to evaluate : 0.966 Fit side-chains REVERT: A 46 HIS cc_start: 0.5935 (OUTLIER) cc_final: 0.5121 (t70) REVERT: A 260 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7786 (mmtp) REVERT: A 572 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: B 214 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8608 (mtpt) REVERT: B 221 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7227 (p0) REVERT: B 279 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7875 (mt-10) outliers start: 43 outliers final: 26 residues processed: 123 average time/residue: 0.2332 time to fit residues: 39.4957 Evaluate side-chains 118 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 86 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 401 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 103 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9561 Z= 0.327 Angle : 0.609 8.149 13168 Z= 0.323 Chirality : 0.044 0.218 1464 Planarity : 0.005 0.054 1526 Dihedral : 17.226 144.767 1787 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.49 % Favored : 91.41 % Rotamer: Outliers : 4.62 % Allowed : 27.48 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -1.12 (0.26), residues: 1036 helix: 1.06 (0.28), residues: 378 sheet: -0.73 (0.40), residues: 185 loop : -2.35 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 377 HIS 0.006 0.001 HIS B 29 PHE 0.019 0.002 PHE A 9 TYR 0.020 0.002 TYR B 341 ARG 0.007 0.001 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 86 time to evaluate : 1.133 Fit side-chains REVERT: A 46 HIS cc_start: 0.5981 (OUTLIER) cc_final: 0.5565 (t70) REVERT: A 133 ASN cc_start: 0.7506 (m-40) cc_final: 0.7175 (m-40) REVERT: A 260 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7687 (mmtp) REVERT: A 572 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: B 214 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8548 (mtpt) REVERT: B 221 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7273 (p0) outliers start: 41 outliers final: 25 residues processed: 118 average time/residue: 0.2431 time to fit residues: 39.7721 Evaluate side-chains 114 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 84 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9561 Z= 0.185 Angle : 0.528 6.600 13168 Z= 0.284 Chirality : 0.041 0.163 1464 Planarity : 0.004 0.034 1526 Dihedral : 16.999 137.966 1787 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.72 % Favored : 92.18 % Rotamer: Outliers : 3.72 % Allowed : 28.72 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.87 (0.26), residues: 1036 helix: 1.27 (0.28), residues: 379 sheet: -0.42 (0.40), residues: 183 loop : -2.27 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 377 HIS 0.003 0.001 HIS A 441 PHE 0.014 0.001 PHE A 328 TYR 0.014 0.001 TYR B 341 ARG 0.009 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 87 time to evaluate : 1.006 Fit side-chains REVERT: A 46 HIS cc_start: 0.5975 (OUTLIER) cc_final: 0.5549 (t70) REVERT: A 133 ASN cc_start: 0.7432 (m-40) cc_final: 0.7121 (m-40) REVERT: A 260 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7647 (mmtp) REVERT: A 572 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: B 176 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7338 (mp) REVERT: B 214 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8588 (mtpt) REVERT: B 221 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7268 (p0) outliers start: 33 outliers final: 21 residues processed: 114 average time/residue: 0.2319 time to fit residues: 36.3116 Evaluate side-chains 113 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 86 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 379 GLN Chi-restraints excluded: chain B residue 401 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.0070 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9561 Z= 0.158 Angle : 0.505 6.376 13168 Z= 0.272 Chirality : 0.040 0.153 1464 Planarity : 0.004 0.037 1526 Dihedral : 16.842 134.183 1786 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.11 % Favored : 91.80 % Rotamer: Outliers : 3.15 % Allowed : 29.39 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.69 (0.27), residues: 1036 helix: 1.45 (0.29), residues: 378 sheet: -0.36 (0.40), residues: 190 loop : -2.19 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 377 HIS 0.003 0.001 HIS A 441 PHE 0.017 0.001 PHE A 91 TYR 0.014 0.001 TYR A 271 ARG 0.009 0.000 ARG B 168 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 0.949 Fit side-chains REVERT: A 46 HIS cc_start: 0.5942 (OUTLIER) cc_final: 0.5506 (t70) REVERT: A 260 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7783 (mmtp) REVERT: A 572 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8212 (tm-30) REVERT: B 176 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7271 (mp) REVERT: B 214 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8620 (mtpt) REVERT: B 221 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7277 (p0) outliers start: 28 outliers final: 18 residues processed: 114 average time/residue: 0.2376 time to fit residues: 36.8886 Evaluate side-chains 110 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 95 optimal weight: 0.0000 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9561 Z= 0.184 Angle : 0.518 6.807 13168 Z= 0.278 Chirality : 0.040 0.159 1464 Planarity : 0.004 0.037 1526 Dihedral : 16.846 136.108 1786 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.53 % Favored : 92.37 % Rotamer: Outliers : 3.94 % Allowed : 28.60 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.27), residues: 1036 helix: 1.42 (0.28), residues: 378 sheet: -0.32 (0.40), residues: 187 loop : -2.16 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 377 HIS 0.003 0.001 HIS B 29 PHE 0.012 0.001 PHE A 328 TYR 0.015 0.001 TYR A 74 ARG 0.009 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 0.993 Fit side-chains REVERT: A 46 HIS cc_start: 0.5936 (OUTLIER) cc_final: 0.5503 (t70) REVERT: A 244 ASN cc_start: 0.6889 (p0) cc_final: 0.6418 (p0) REVERT: A 260 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7795 (mmtp) REVERT: A 328 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.5866 (t80) REVERT: A 572 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: B 176 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7261 (mp) REVERT: B 214 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8597 (mtpt) REVERT: B 221 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7274 (p0) REVERT: B 279 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7859 (mt-10) outliers start: 35 outliers final: 24 residues processed: 116 average time/residue: 0.2245 time to fit residues: 36.1134 Evaluate side-chains 118 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 86 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 70 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS B 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9561 Z= 0.161 Angle : 0.512 6.653 13168 Z= 0.275 Chirality : 0.040 0.155 1464 Planarity : 0.004 0.039 1526 Dihedral : 16.832 135.478 1786 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.53 % Favored : 92.37 % Rotamer: Outliers : 3.94 % Allowed : 28.83 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.64 (0.27), residues: 1036 helix: 1.43 (0.28), residues: 379 sheet: -0.29 (0.40), residues: 187 loop : -2.14 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 377 HIS 0.003 0.001 HIS A 441 PHE 0.013 0.001 PHE A 91 TYR 0.014 0.001 TYR A 74 ARG 0.011 0.000 ARG A 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 87 time to evaluate : 0.995 Fit side-chains REVERT: A 46 HIS cc_start: 0.5898 (OUTLIER) cc_final: 0.5465 (t70) REVERT: A 244 ASN cc_start: 0.6880 (p0) cc_final: 0.6410 (p0) REVERT: A 260 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7785 (mmtp) REVERT: A 328 PHE cc_start: 0.6130 (OUTLIER) cc_final: 0.5759 (t80) REVERT: A 572 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: B 176 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7244 (mp) REVERT: B 214 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8603 (mtpt) REVERT: B 221 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7271 (p0) REVERT: B 279 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7824 (mt-10) outliers start: 35 outliers final: 23 residues processed: 115 average time/residue: 0.2282 time to fit residues: 36.3427 Evaluate side-chains 117 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 86 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 421 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 87 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.168018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.129362 restraints weight = 10934.173| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.73 r_work: 0.3142 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9561 Z= 0.164 Angle : 0.507 6.509 13168 Z= 0.272 Chirality : 0.040 0.146 1464 Planarity : 0.004 0.038 1526 Dihedral : 16.765 134.116 1786 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.63 % Favored : 92.28 % Rotamer: Outliers : 3.72 % Allowed : 29.05 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -0.61 (0.27), residues: 1036 helix: 1.47 (0.29), residues: 379 sheet: -0.28 (0.40), residues: 190 loop : -2.14 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 377 HIS 0.003 0.001 HIS A 441 PHE 0.011 0.001 PHE A 328 TYR 0.013 0.001 TYR A 74 ARG 0.010 0.000 ARG A 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2239.34 seconds wall clock time: 40 minutes 35.68 seconds (2435.68 seconds total)