Starting phenix.real_space_refine on Fri Jan 19 02:02:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x07_32919/01_2024/7x07_32919_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x07_32919/01_2024/7x07_32919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x07_32919/01_2024/7x07_32919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x07_32919/01_2024/7x07_32919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x07_32919/01_2024/7x07_32919_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x07_32919/01_2024/7x07_32919_updated.pdb" } resolution = 3.78 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= -0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6489 2.51 5 N 1782 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ASP 187": "OD1" <-> "OD2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A ARG 324": "NH1" <-> "NH2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 363": "OE1" <-> "OE2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A ARG 568": "NH1" <-> "NH2" Residue "A TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A ASP 629": "OD1" <-> "OD2" Residue "A GLU 700": "OE1" <-> "OE2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B GLU 331": "OE1" <-> "OE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ASP 555": "OD1" <-> "OD2" Residue "B ASP 561": "OD1" <-> "OD2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B GLU 573": "OE1" <-> "OE2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 622": "NH1" <-> "NH2" Residue "B ASP 629": "OD1" <-> "OD2" Residue "B GLU 630": "OE1" <-> "OE2" Residue "B ASP 649": "OD1" <-> "OD2" Residue "B ASP 674": "OD1" <-> "OD2" Residue "B ARG 712": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10125 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5046 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 22, 'TRANS': 610} Chain breaks: 1 Chain: "B" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5051 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 22, 'TRANS': 610} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'7PO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.54, per 1000 atoms: 0.55 Number of scatterers: 10125 At special positions: 0 Unit cell: (74.7, 118.69, 147.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1806 8.00 N 1782 7.00 C 6489 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: 3.51 Conformation dependent library (CDL) restraints added in 1.7 seconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 3 sheets defined 43.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 69 through 82 removed outlier: 3.960A pdb=" N GLN A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 removed outlier: 3.741A pdb=" N LEU A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 105 No H-bonds generated for 'chain 'A' and resid 102 through 105' Processing helix chain 'A' and resid 107 through 110 No H-bonds generated for 'chain 'A' and resid 107 through 110' Processing helix chain 'A' and resid 116 through 123 removed outlier: 4.397A pdb=" N CYS A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 167 removed outlier: 3.650A pdb=" N GLY A 131 " --> pdb=" O PRO A 127 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TRP A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 143 - end of helix removed outlier: 3.872A pdb=" N ARG A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 174 No H-bonds generated for 'chain 'A' and resid 171 through 174' Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.055A pdb=" N SER A 184 " --> pdb=" O TYR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 202 through 205 No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 218 through 235 removed outlier: 4.089A pdb=" N ALA A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 262 through 268 removed outlier: 4.020A pdb=" N GLU A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 295 No H-bonds generated for 'chain 'A' and resid 292 through 295' Processing helix chain 'A' and resid 303 through 306 No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 340 through 352 removed outlier: 3.663A pdb=" N ALA A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.825A pdb=" N GLU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.908A pdb=" N ALA A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 removed outlier: 4.320A pdb=" N ILE A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 431 removed outlier: 3.531A pdb=" N THR A 410 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 411 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 416 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 417 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 421 " --> pdb=" O ARG A 418 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE A 426 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 427 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 429 " --> pdb=" O PHE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 553 through 558 removed outlier: 4.169A pdb=" N VAL A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 553 through 558' Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 586 through 590 Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.695A pdb=" N LYS A 610 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLN A 611 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 613 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 661 through 666 removed outlier: 3.767A pdb=" N LYS A 665 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 700 removed outlier: 4.476A pdb=" N LYS A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 720 removed outlier: 4.285A pdb=" N ILE A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.774A pdb=" N TRP B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 128 through 138 removed outlier: 3.715A pdb=" N TRP B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN B 136 " --> pdb=" O TRP B 132 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 137 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 145 No H-bonds generated for 'chain 'B' and resid 142 through 145' Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 182 through 185 No H-bonds generated for 'chain 'B' and resid 182 through 185' Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.629A pdb=" N THR B 198 " --> pdb=" O ASP B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 207 Processing helix chain 'B' and resid 221 through 224 No H-bonds generated for 'chain 'B' and resid 221 through 224' Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 251 through 254 No H-bonds generated for 'chain 'B' and resid 251 through 254' Processing helix chain 'B' and resid 268 through 288 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 328 through 336 removed outlier: 3.946A pdb=" N LEU B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 352 removed outlier: 4.319A pdb=" N LEU B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 363 through 370 Processing helix chain 'B' and resid 374 through 377 Processing helix chain 'B' and resid 383 through 392 removed outlier: 4.218A pdb=" N ALA B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 431 removed outlier: 4.350A pdb=" N ALA B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 424 " --> pdb=" O HIS B 420 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 521 removed outlier: 4.369A pdb=" N PHE B 517 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 555 No H-bonds generated for 'chain 'B' and resid 553 through 555' Processing helix chain 'B' and resid 565 through 567 No H-bonds generated for 'chain 'B' and resid 565 through 567' Processing helix chain 'B' and resid 573 through 582 removed outlier: 4.134A pdb=" N VAL B 582 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 620 removed outlier: 3.749A pdb=" N MET B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 650 Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 687 through 720 removed outlier: 3.889A pdb=" N SER B 691 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 706 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Proline residue: B 707 - end of helix removed outlier: 5.744A pdb=" N GLN B 710 " --> pdb=" O ILE B 706 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG B 711 " --> pdb=" O PRO B 707 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ARG B 712 " --> pdb=" O LYS B 708 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 713 " --> pdb=" O MET B 709 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 714 " --> pdb=" O GLN B 710 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU B 715 " --> pdb=" O ARG B 711 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 719 " --> pdb=" O GLU B 715 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 466 through 469 removed outlier: 4.836A pdb=" N LEU A 493 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 467 through 469 removed outlier: 6.517A pdb=" N LEU B 531 " --> pdb=" O VAL B 468 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 539 through 543 removed outlier: 7.089A pdb=" N TYR B 625 " --> pdb=" O PHE B 540 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE B 542 " --> pdb=" O TYR B 625 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU B 627 " --> pdb=" O ILE B 542 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 247 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1626 1.30 - 1.43: 2748 1.43 - 1.56: 5880 1.56 - 1.69: 0 1.69 - 1.83: 80 Bond restraints: 10334 Sorted by residual: bond pdb=" C PRO B 143 " pdb=" O PRO B 143 " ideal model delta sigma weight residual 1.238 1.170 0.068 1.37e-02 5.33e+03 2.48e+01 bond pdb=" N ARG B 236 " pdb=" CA ARG B 236 " ideal model delta sigma weight residual 1.459 1.519 -0.060 1.23e-02 6.61e+03 2.38e+01 bond pdb=" C VAL A 224 " pdb=" O VAL A 224 " ideal model delta sigma weight residual 1.231 1.278 -0.047 1.02e-02 9.61e+03 2.11e+01 bond pdb=" C ALA B 626 " pdb=" O ALA B 626 " ideal model delta sigma weight residual 1.235 1.184 0.051 1.15e-02 7.56e+03 1.99e+01 bond pdb=" N THR B 506 " pdb=" CA THR B 506 " ideal model delta sigma weight residual 1.455 1.510 -0.055 1.27e-02 6.20e+03 1.86e+01 ... (remaining 10329 not shown) Histogram of bond angle deviations from ideal: 92.03 - 100.51: 21 100.51 - 109.00: 932 109.00 - 117.48: 6512 117.48 - 125.97: 6316 125.97 - 134.45: 189 Bond angle restraints: 13970 Sorted by residual: angle pdb=" N ILE B 637 " pdb=" CA ILE B 637 " pdb=" C ILE B 637 " ideal model delta sigma weight residual 109.34 92.03 17.31 2.08e+00 2.31e-01 6.93e+01 angle pdb=" N ILE A 320 " pdb=" CA ILE A 320 " pdb=" C ILE A 320 " ideal model delta sigma weight residual 112.17 105.61 6.56 9.50e-01 1.11e+00 4.77e+01 angle pdb=" N ILE B 151 " pdb=" CA ILE B 151 " pdb=" C ILE B 151 " ideal model delta sigma weight residual 112.90 106.87 6.03 9.60e-01 1.09e+00 3.95e+01 angle pdb=" N ALA B 168 " pdb=" CA ALA B 168 " pdb=" C ALA B 168 " ideal model delta sigma weight residual 112.68 104.44 8.24 1.33e+00 5.65e-01 3.84e+01 angle pdb=" N VAL B 102 " pdb=" CA VAL B 102 " pdb=" C VAL B 102 " ideal model delta sigma weight residual 111.91 106.50 5.41 8.90e-01 1.26e+00 3.70e+01 ... (remaining 13965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 5475 17.58 - 35.15: 605 35.15 - 52.73: 113 52.73 - 70.30: 19 70.30 - 87.88: 14 Dihedral angle restraints: 6226 sinusoidal: 2544 harmonic: 3682 Sorted by residual: dihedral pdb=" CA LEU B 96 " pdb=" C LEU B 96 " pdb=" N HIS B 97 " pdb=" CA HIS B 97 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ALA B 170 " pdb=" C ALA B 170 " pdb=" N TYR B 171 " pdb=" CA TYR B 171 " ideal model delta harmonic sigma weight residual 180.00 153.04 26.96 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA SER B 636 " pdb=" C SER B 636 " pdb=" N ILE B 637 " pdb=" CA ILE B 637 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 6223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 921 0.067 - 0.134: 511 0.134 - 0.201: 119 0.201 - 0.267: 7 0.267 - 0.334: 1 Chirality restraints: 1559 Sorted by residual: chirality pdb=" CA ILE B 637 " pdb=" N ILE B 637 " pdb=" C ILE B 637 " pdb=" CB ILE B 637 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB THR A 225 " pdb=" CA THR A 225 " pdb=" OG1 THR A 225 " pdb=" CG2 THR A 225 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE A 657 " pdb=" N ILE A 657 " pdb=" C ILE A 657 " pdb=" CB ILE A 657 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1556 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 143 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C PRO B 143 " 0.065 2.00e-02 2.50e+03 pdb=" O PRO B 143 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 144 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 641 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLY B 641 " 0.061 2.00e-02 2.50e+03 pdb=" O GLY B 641 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS B 642 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 622 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C ARG B 622 " 0.061 2.00e-02 2.50e+03 pdb=" O ARG B 622 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO B 623 " -0.020 2.00e-02 2.50e+03 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 311 2.70 - 3.25: 10044 3.25 - 3.80: 14795 3.80 - 4.35: 20469 4.35 - 4.90: 32203 Nonbonded interactions: 77822 Sorted by model distance: nonbonded pdb=" N ILE B 637 " pdb=" O ILE B 637 " model vdw 2.145 2.496 nonbonded pdb=" C SER B 636 " pdb=" O ILE B 637 " model vdw 2.211 3.270 nonbonded pdb=" NH1 ARG B 275 " pdb=" O ASP B 312 " model vdw 2.319 2.520 nonbonded pdb=" O GLY A 188 " pdb=" NH2 ARG A 191 " model vdw 2.325 2.520 nonbonded pdb=" OE2 GLU B 155 " pdb=" OG SER B 213 " model vdw 2.335 2.440 ... (remaining 77817 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 67 through 721) selection = (chain 'B' and resid 67 through 721) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 11.740 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.180 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 : 0.013 0.068 10334 Z= 0.837 Angle : 1.657 17.311 13970 Z= 1.222 Chirality : 0.077 0.334 1559 Planarity : 0.008 0.046 1774 Dihedral : 15.382 87.879 3856 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.11 % Favored : 91.18 % Rotamer: Outliers : 1.97 % Allowed : 5.53 % Favored : 92.50 % 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: -4.75 (0.20), residues: 1258 helix: -3.09 (0.15), residues: 739 sheet: -3.69 (0.77), residues: 40 loop : -2.93 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.005 TRP B 524 HIS 0.020 0.004 HIS B 621 PHE 0.042 0.005 PHE B 204 TYR 0.036 0.006 TYR B 174 ARG 0.015 0.002 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 LEU cc_start: 0.9135 (tp) cc_final: 0.8910 (tt) REVERT: B 160 LEU cc_start: 0.8818 (tp) cc_final: 0.8434 (tt) REVERT: B 493 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7664 (mp) REVERT: B 501 MET cc_start: 0.7923 (tpp) cc_final: 0.7208 (mmm) REVERT: B 615 MET cc_start: 0.7873 (mtt) cc_final: 0.7389 (mtt) REVERT: B 663 LEU cc_start: 0.9145 (tp) cc_final: 0.8939 (tt) outliers start: 21 outliers final: 8 residues processed: 161 average time/residue: 0.2296 time to fit residues: 51.8062 Evaluate side-chains 120 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 621 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.0870 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 98 optimal weight: 0.2980 chunk 38 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN B 645 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10334 Z= 0.193 Angle : 0.678 10.809 13970 Z= 0.359 Chirality : 0.041 0.139 1559 Planarity : 0.004 0.035 1774 Dihedral : 7.726 56.898 1454 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.92 % Favored : 92.85 % Rotamer: Outliers : 1.59 % Allowed : 10.59 % Favored : 87.82 % 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: -4.10 (0.22), residues: 1258 helix: -2.58 (0.17), residues: 763 sheet: -2.41 (0.94), residues: 33 loop : -2.71 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 664 HIS 0.007 0.001 HIS B 621 PHE 0.016 0.001 PHE A 146 TYR 0.017 0.001 TYR B 620 ARG 0.007 0.001 ARG B 545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.5693 (tpt) cc_final: 0.5454 (mmm) REVERT: A 505 ILE cc_start: 0.5932 (OUTLIER) cc_final: 0.5626 (mt) REVERT: A 537 GLN cc_start: 0.6002 (mm-40) cc_final: 0.5384 (tp40) REVERT: A 674 ASP cc_start: 0.5801 (p0) cc_final: 0.5361 (p0) REVERT: B 493 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7623 (mp) REVERT: B 501 MET cc_start: 0.7822 (tpp) cc_final: 0.7435 (mmt) REVERT: B 663 LEU cc_start: 0.9097 (tp) cc_final: 0.8847 (tt) outliers start: 17 outliers final: 10 residues processed: 140 average time/residue: 0.2107 time to fit residues: 42.7755 Evaluate side-chains 130 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 621 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 chunk 91 optimal weight: 0.0770 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN B 433 HIS B 584 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10334 Z= 0.243 Angle : 0.632 10.943 13970 Z= 0.332 Chirality : 0.043 0.213 1559 Planarity : 0.004 0.049 1774 Dihedral : 7.337 59.850 1445 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.03 % Favored : 91.89 % Rotamer: Outliers : 2.25 % Allowed : 13.21 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.22), residues: 1258 helix: -2.39 (0.17), residues: 769 sheet: -2.61 (0.96), residues: 34 loop : -2.63 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 664 HIS 0.006 0.001 HIS B 621 PHE 0.033 0.002 PHE A 681 TYR 0.012 0.001 TYR A 153 ARG 0.007 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 505 ILE cc_start: 0.5910 (OUTLIER) cc_final: 0.5643 (mt) REVERT: A 548 MET cc_start: 0.6362 (tmm) cc_final: 0.6109 (tmm) REVERT: B 335 MET cc_start: 0.7134 (tmm) cc_final: 0.6843 (ttm) REVERT: B 493 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7518 (mp) REVERT: B 501 MET cc_start: 0.7955 (tpp) cc_final: 0.7419 (mmm) outliers start: 24 outliers final: 11 residues processed: 135 average time/residue: 0.2022 time to fit residues: 39.7679 Evaluate side-chains 111 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 621 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 30.0000 chunk 76 optimal weight: 0.2980 chunk 115 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN B 148 ASN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10334 Z= 0.202 Angle : 0.606 11.891 13970 Z= 0.314 Chirality : 0.041 0.148 1559 Planarity : 0.004 0.044 1774 Dihedral : 6.971 55.553 1445 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.39 % Favored : 92.53 % Rotamer: Outliers : 2.16 % Allowed : 15.46 % Favored : 82.38 % 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: -3.68 (0.22), residues: 1258 helix: -2.23 (0.17), residues: 772 sheet: -2.59 (0.80), residues: 44 loop : -2.51 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 137 HIS 0.011 0.001 HIS B 669 PHE 0.016 0.001 PHE A 252 TYR 0.010 0.001 TYR B 174 ARG 0.004 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 319 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8874 (tt) REVERT: A 322 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8714 (tp) REVERT: A 505 ILE cc_start: 0.5886 (OUTLIER) cc_final: 0.5674 (mt) REVERT: A 548 MET cc_start: 0.6220 (tmm) cc_final: 0.5966 (tmm) REVERT: B 335 MET cc_start: 0.7219 (tmm) cc_final: 0.6889 (ttm) REVERT: B 380 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7223 (tt0) REVERT: B 501 MET cc_start: 0.8257 (tpp) cc_final: 0.7861 (tpp) outliers start: 23 outliers final: 12 residues processed: 118 average time/residue: 0.1994 time to fit residues: 35.2426 Evaluate side-chains 113 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 621 HIS Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10334 Z= 0.217 Angle : 0.592 11.890 13970 Z= 0.306 Chirality : 0.041 0.126 1559 Planarity : 0.004 0.047 1774 Dihedral : 6.723 55.146 1443 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.79 % Favored : 92.13 % Rotamer: Outliers : 2.81 % Allowed : 15.84 % Favored : 81.35 % 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: -3.57 (0.22), residues: 1258 helix: -2.09 (0.18), residues: 768 sheet: -2.54 (0.93), residues: 34 loop : -2.61 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 137 HIS 0.006 0.001 HIS B 669 PHE 0.015 0.001 PHE A 252 TYR 0.010 0.001 TYR B 174 ARG 0.005 0.000 ARG B 163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 161 SER cc_start: 0.7040 (OUTLIER) cc_final: 0.6646 (t) REVERT: A 319 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8866 (tt) REVERT: A 548 MET cc_start: 0.6205 (tmm) cc_final: 0.5989 (tmm) REVERT: B 335 MET cc_start: 0.7265 (tmm) cc_final: 0.6914 (ttm) REVERT: B 380 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7205 (tt0) REVERT: B 683 LYS cc_start: 0.8437 (tptt) cc_final: 0.8233 (tptt) outliers start: 30 outliers final: 21 residues processed: 133 average time/residue: 0.2004 time to fit residues: 39.5233 Evaluate side-chains 124 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 621 HIS Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 9.9990 chunk 109 optimal weight: 0.0000 chunk 24 optimal weight: 0.0170 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 overall best weight: 0.4422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN B 148 ASN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10334 Z= 0.167 Angle : 0.576 11.696 13970 Z= 0.297 Chirality : 0.040 0.167 1559 Planarity : 0.003 0.038 1774 Dihedral : 6.356 57.275 1441 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.15 % Favored : 92.77 % Rotamer: Outliers : 2.16 % Allowed : 17.43 % Favored : 80.41 % 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: -3.40 (0.23), residues: 1258 helix: -1.93 (0.18), residues: 765 sheet: -2.52 (0.92), residues: 34 loop : -2.59 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 77 HIS 0.008 0.001 HIS B 669 PHE 0.017 0.001 PHE A 252 TYR 0.008 0.001 TYR B 181 ARG 0.008 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 319 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8751 (tt) REVERT: B 335 MET cc_start: 0.7240 (tmm) cc_final: 0.6895 (ttm) REVERT: B 380 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7154 (tt0) REVERT: B 683 LYS cc_start: 0.8246 (tptt) cc_final: 0.7999 (tptt) outliers start: 23 outliers final: 18 residues processed: 130 average time/residue: 0.1925 time to fit residues: 37.3598 Evaluate side-chains 126 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 604 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 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 332 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10334 Z= 0.219 Angle : 0.598 11.784 13970 Z= 0.305 Chirality : 0.042 0.147 1559 Planarity : 0.004 0.045 1774 Dihedral : 6.401 59.106 1439 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.34 % Allowed : 18.09 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.23), residues: 1258 helix: -1.85 (0.18), residues: 773 sheet: -2.50 (0.92), residues: 34 loop : -2.57 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 524 HIS 0.006 0.001 HIS B 621 PHE 0.017 0.001 PHE A 252 TYR 0.009 0.001 TYR B 174 ARG 0.007 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 253 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6235 (tp) REVERT: A 319 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8772 (tt) REVERT: A 517 PHE cc_start: 0.6333 (OUTLIER) cc_final: 0.6077 (t80) REVERT: B 335 MET cc_start: 0.7263 (tmm) cc_final: 0.6918 (ttm) REVERT: B 380 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7203 (tt0) REVERT: B 683 LYS cc_start: 0.8318 (tptt) cc_final: 0.8079 (tptt) outliers start: 25 outliers final: 19 residues processed: 129 average time/residue: 0.1977 time to fit residues: 37.7537 Evaluate side-chains 124 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 604 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10334 Z= 0.207 Angle : 0.588 11.832 13970 Z= 0.300 Chirality : 0.041 0.136 1559 Planarity : 0.004 0.039 1774 Dihedral : 6.287 58.025 1439 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.44 % Allowed : 18.37 % Favored : 79.19 % 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: -3.20 (0.23), residues: 1258 helix: -1.74 (0.18), residues: 770 sheet: -2.51 (0.77), residues: 51 loop : -2.51 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 137 HIS 0.006 0.001 HIS B 669 PHE 0.025 0.001 PHE A 71 TYR 0.008 0.001 TYR B 174 ARG 0.007 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 161 SER cc_start: 0.7200 (OUTLIER) cc_final: 0.6660 (t) REVERT: A 319 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8756 (tt) REVERT: A 517 PHE cc_start: 0.6315 (OUTLIER) cc_final: 0.5969 (t80) REVERT: B 335 MET cc_start: 0.7280 (tmm) cc_final: 0.6990 (ttm) REVERT: B 380 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7138 (tt0) outliers start: 26 outliers final: 22 residues processed: 121 average time/residue: 0.2038 time to fit residues: 36.6107 Evaluate side-chains 124 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 604 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 49 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 0.0670 chunk 112 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 332 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10334 Z= 0.182 Angle : 0.586 11.633 13970 Z= 0.297 Chirality : 0.040 0.130 1559 Planarity : 0.004 0.042 1774 Dihedral : 6.068 54.119 1439 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.62 % Allowed : 18.18 % Favored : 79.19 % 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: -3.07 (0.23), residues: 1258 helix: -1.64 (0.18), residues: 770 sheet: -2.33 (0.80), residues: 50 loop : -2.50 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 137 HIS 0.006 0.001 HIS B 669 PHE 0.016 0.001 PHE A 252 TYR 0.007 0.001 TYR B 174 ARG 0.007 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: A 161 SER cc_start: 0.7158 (OUTLIER) cc_final: 0.6629 (t) REVERT: A 253 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6363 (tp) REVERT: A 319 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8718 (tt) REVERT: A 517 PHE cc_start: 0.6245 (OUTLIER) cc_final: 0.5962 (t80) REVERT: B 329 MET cc_start: 0.7803 (tpp) cc_final: 0.7454 (tpp) REVERT: B 335 MET cc_start: 0.7279 (tmm) cc_final: 0.6997 (ttm) REVERT: B 342 SER cc_start: 0.8623 (m) cc_final: 0.7863 (t) REVERT: B 380 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7157 (tt0) outliers start: 28 outliers final: 20 residues processed: 130 average time/residue: 0.1928 time to fit residues: 37.2550 Evaluate side-chains 125 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.1980 chunk 56 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN A 332 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10334 Z= 0.249 Angle : 0.625 11.251 13970 Z= 0.315 Chirality : 0.043 0.226 1559 Planarity : 0.004 0.041 1774 Dihedral : 6.290 52.539 1439 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.44 % Allowed : 18.65 % Favored : 78.91 % 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: -3.10 (0.23), residues: 1258 helix: -1.64 (0.18), residues: 773 sheet: -2.34 (0.85), residues: 44 loop : -2.57 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 595 HIS 0.009 0.001 HIS B 669 PHE 0.018 0.001 PHE A 252 TYR 0.013 0.001 TYR B 181 ARG 0.007 0.000 ARG A 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 161 SER cc_start: 0.7171 (OUTLIER) cc_final: 0.6596 (t) REVERT: A 253 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6475 (tp) REVERT: A 319 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8725 (tt) REVERT: A 338 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.7217 (m) REVERT: A 517 PHE cc_start: 0.6339 (OUTLIER) cc_final: 0.6089 (t80) REVERT: B 81 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8699 (tp) REVERT: B 329 MET cc_start: 0.7829 (tpp) cc_final: 0.7487 (tpp) REVERT: B 335 MET cc_start: 0.7305 (tmm) cc_final: 0.7030 (ttm) REVERT: B 342 SER cc_start: 0.8567 (m) cc_final: 0.7761 (t) REVERT: B 380 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7200 (tt0) outliers start: 26 outliers final: 20 residues processed: 128 average time/residue: 0.2008 time to fit residues: 38.0797 Evaluate side-chains 129 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN B 148 ASN ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.256983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.220824 restraints weight = 11092.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.218611 restraints weight = 16531.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.215687 restraints weight = 16553.252| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10334 Z= 0.195 Angle : 0.593 10.754 13970 Z= 0.301 Chirality : 0.041 0.157 1559 Planarity : 0.004 0.040 1774 Dihedral : 6.086 49.929 1439 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.34 % Allowed : 18.93 % Favored : 78.73 % 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: -2.99 (0.23), residues: 1258 helix: -1.54 (0.19), residues: 767 sheet: -2.42 (0.84), residues: 44 loop : -2.53 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 77 HIS 0.008 0.001 HIS B 669 PHE 0.017 0.001 PHE A 252 TYR 0.013 0.001 TYR B 181 ARG 0.007 0.000 ARG B 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2106.83 seconds wall clock time: 38 minutes 59.76 seconds (2339.76 seconds total)