Starting phenix.real_space_refine on Fri Mar 22 20:49:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhx_12342/03_2024/7nhx_12342.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhx_12342/03_2024/7nhx_12342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhx_12342/03_2024/7nhx_12342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhx_12342/03_2024/7nhx_12342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhx_12342/03_2024/7nhx_12342.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhx_12342/03_2024/7nhx_12342.pdb" } resolution = 3.23 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= 0.018 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: 6 Type Number sf(0) Gaussians P 23 5.49 5 S 123 5.16 5 C 10942 2.51 5 N 3070 2.21 5 O 3354 1.98 5 H 17149 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ASP 347": "OD1" <-> "OD2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A ASP 514": "OD1" <-> "OD2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B ASP 130": "OD1" <-> "OD2" Residue "B ASP 165": "OD1" <-> "OD2" Residue "B TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 608": "OE1" <-> "OE2" Residue "B TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C ASP 60": "OD1" <-> "OD2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C ASP 309": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34661 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11524 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "B" Number of atoms: 11619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 11619 Classifications: {'peptide': 729} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 30, 'TRANS': 698} Chain breaks: 2 Chain: "C" Number of atoms: 10772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 10772 Classifications: {'peptide': 676} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 27, 'TRANS': 648} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 255 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "F" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 491 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 11} Time building chain proxies: 15.24, per 1000 atoms: 0.44 Number of scatterers: 34661 At special positions: 0 Unit cell: (130.35, 105.6, 146.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 123 16.00 P 23 15.00 O 3354 8.00 N 3070 7.00 C 10942 6.00 H 17149 1.00 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: 27.62 Conformation dependent library (CDL) restraints added in 3.1 seconds 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4000 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 24 sheets defined 50.1% alpha, 12.2% beta 3 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 15.00 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.757A pdb=" N PHE A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 24 removed outlier: 4.103A pdb=" N TYR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 50 removed outlier: 3.512A pdb=" N ALA A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 removed outlier: 4.050A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.894A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 removed outlier: 3.839A pdb=" N SER A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.967A pdb=" N GLU A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.634A pdb=" N THR A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.665A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.366A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 4.017A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.639A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 removed outlier: 3.671A pdb=" N LYS A 615 " --> pdb=" O PHE A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.669A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 691 removed outlier: 3.628A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 138 through 154 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.911A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 246 through 265 removed outlier: 4.207A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 291 Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.576A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.587A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.522A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.824A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 573 through 583 removed outlier: 3.792A pdb=" N LYS B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.758A pdb=" N GLY B 588 " --> pdb=" O SER B 585 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 589' Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.582A pdb=" N GLY B 594 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.514A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 removed outlier: 3.786A pdb=" N LYS B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.681A pdb=" N VAL B 640 " --> pdb=" O ILE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 677 removed outlier: 3.628A pdb=" N ASN B 676 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.264A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.146A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 removed outlier: 4.019A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 49 Processing helix chain 'C' and resid 50 through 53 Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.602A pdb=" N THR C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 4.061A pdb=" N LYS C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.789A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.709A pdb=" N GLU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.721A pdb=" N GLU C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 251 through 273 removed outlier: 3.533A pdb=" N VAL C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 305 through 315 Processing helix chain 'C' and resid 390 through 406 removed outlier: 3.652A pdb=" N GLN C 406 " --> pdb=" O MET C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 429 through 438 Processing helix chain 'C' and resid 442 through 450 removed outlier: 4.789A pdb=" N GLY C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 460 removed outlier: 3.960A pdb=" N GLY C 459 " --> pdb=" O ASN C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 556 Processing helix chain 'C' and resid 556 through 564 removed outlier: 4.352A pdb=" N ILE C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 573 Processing helix chain 'C' and resid 577 through 583 removed outlier: 3.537A pdb=" N LEU C 583 " --> pdb=" O PRO C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 606 removed outlier: 4.613A pdb=" N GLN C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 606 " --> pdb=" O GLN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 622 No H-bonds generated for 'chain 'C' and resid 620 through 622' Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.767A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 removed outlier: 3.819A pdb=" N TYR B 483 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.710A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 324 removed outlier: 3.828A pdb=" N ASN A 321 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 542 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 378 removed outlier: 6.062A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 619 through 623 removed outlier: 6.094A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 185 removed outlier: 3.532A pdb=" N GLY B 206 " --> pdb=" O PHE B 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.901A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 643 Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 4.543A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB7, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AB8, first strand: chain 'C' and resid 319 through 320 Processing sheet with id=AB9, first strand: chain 'C' and resid 324 through 325 Processing sheet with id=AC1, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.142A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR C 371 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL C 386 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 373 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU C 384 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG C 375 " --> pdb=" O ILE C 382 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 342 through 345 Processing sheet with id=AC3, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.738A pdb=" N SER C 474 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 504 through 505 removed outlier: 6.496A pdb=" N VAL C 504 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 635 through 640 Processing sheet with id=AC6, first strand: chain 'C' and resid 657 through 658 removed outlier: 5.925A pdb=" N LEU C 665 " --> pdb=" O ALA C 672 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2256 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 3 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 12.81 Time building geometry restraints manager: 28.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 17119 1.00 - 1.21: 30 1.21 - 1.41: 7229 1.41 - 1.62: 10454 1.62 - 1.82: 216 Bond restraints: 35048 Sorted by residual: bond pdb=" NE2 GLN C 581 " pdb="HE22 GLN C 581 " ideal model delta sigma weight residual 0.860 0.800 0.060 2.00e-02 2.50e+03 9.01e+00 bond pdb=" NE2 GLN C 426 " pdb="HE22 GLN C 426 " ideal model delta sigma weight residual 0.860 0.804 0.056 2.00e-02 2.50e+03 7.97e+00 bond pdb=" ND2 ASN C 422 " pdb="HD22 ASN C 422 " ideal model delta sigma weight residual 0.860 0.822 0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" CB PRO C 453 " pdb=" CG PRO C 453 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.03e+00 bond pdb=" ND2 ASN C 540 " pdb="HD22 ASN C 540 " ideal model delta sigma weight residual 0.860 0.828 0.032 2.00e-02 2.50e+03 2.62e+00 ... (remaining 35043 not shown) Histogram of bond angle deviations from ideal: 73.56 - 87.03: 3 87.03 - 100.49: 19 100.49 - 113.95: 42518 113.95 - 127.42: 20500 127.42 - 140.88: 223 Bond angle restraints: 63263 Sorted by residual: angle pdb=" N MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 110.00 73.56 36.44 3.00e+00 1.11e-01 1.48e+02 angle pdb=" C MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 110.00 74.77 35.23 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 109.00 73.86 35.14 3.00e+00 1.11e-01 1.37e+02 angle pdb=" CD GLN C 426 " pdb=" NE2 GLN C 426 " pdb="HE22 GLN C 426 " ideal model delta sigma weight residual 120.00 140.88 -20.88 3.00e+00 1.11e-01 4.84e+01 angle pdb="HE21 GLN C 426 " pdb=" NE2 GLN C 426 " pdb="HE22 GLN C 426 " ideal model delta sigma weight residual 120.00 99.17 20.83 3.00e+00 1.11e-01 4.82e+01 ... (remaining 63258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14762 17.98 - 35.96: 1268 35.96 - 53.95: 310 53.95 - 71.93: 108 71.93 - 89.91: 23 Dihedral angle restraints: 16471 sinusoidal: 9309 harmonic: 7162 Sorted by residual: dihedral pdb=" CA GLN A 180 " pdb=" C GLN A 180 " pdb=" N GLU A 181 " pdb=" CA GLU A 181 " ideal model delta harmonic sigma weight residual 180.00 155.20 24.80 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA GLU A 126 " pdb=" C GLU A 126 " pdb=" N VAL A 127 " pdb=" CA VAL A 127 " ideal model delta harmonic sigma weight residual -180.00 -155.87 -24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA VAL A 127 " pdb=" C VAL A 127 " pdb=" N HIS A 128 " pdb=" CA HIS A 128 " ideal model delta harmonic sigma weight residual -180.00 -158.89 -21.11 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 16468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2236 0.054 - 0.109: 376 0.109 - 0.163: 68 0.163 - 0.217: 3 0.217 - 0.272: 2 Chirality restraints: 2685 Sorted by residual: chirality pdb=" CG LEU C 183 " pdb=" CB LEU C 183 " pdb=" CD1 LEU C 183 " pdb=" CD2 LEU C 183 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA MET C 536 " pdb=" N MET C 536 " pdb=" C MET C 536 " pdb=" CB MET C 536 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA LYS C 187 " pdb=" N LYS C 187 " pdb=" C LYS C 187 " pdb=" CB LYS C 187 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2682 not shown) Planarity restraints: 5092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 581 " 0.067 2.00e-02 2.50e+03 9.58e-02 1.38e+02 pdb=" CD GLN C 581 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLN C 581 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN C 581 " -0.158 2.00e-02 2.50e+03 pdb="HE21 GLN C 581 " -0.026 2.00e-02 2.50e+03 pdb="HE22 GLN C 581 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 422 " -0.048 2.00e-02 2.50e+03 9.22e-02 1.27e+02 pdb=" CG ASN C 422 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN C 422 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 422 " -0.156 2.00e-02 2.50e+03 pdb="HD21 ASN C 422 " -0.027 2.00e-02 2.50e+03 pdb="HD22 ASN C 422 " 0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 426 " 0.049 2.00e-02 2.50e+03 9.19e-02 1.27e+02 pdb=" CD GLN C 426 " 0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN C 426 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN C 426 " -0.161 2.00e-02 2.50e+03 pdb="HE21 GLN C 426 " -0.035 2.00e-02 2.50e+03 pdb="HE22 GLN C 426 " 0.145 2.00e-02 2.50e+03 ... (remaining 5089 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 935 2.12 - 2.74: 61900 2.74 - 3.36: 99780 3.36 - 3.98: 127647 3.98 - 4.60: 201966 Nonbonded interactions: 492228 Sorted by model distance: nonbonded pdb="HH12 ARG B 706 " pdb=" OE1 GLN C 160 " model vdw 1.496 1.850 nonbonded pdb=" OD2 ASP C 499 " pdb="HH21 ARG C 503 " model vdw 1.506 1.850 nonbonded pdb=" H ASN A 513 " pdb=" OD2 ASP A 516 " model vdw 1.511 1.850 nonbonded pdb=" OD1 ASN B 136 " pdb="HD21 ASN B 225 " model vdw 1.534 1.850 nonbonded pdb="HD22 ASN B 676 " pdb=" O4' U E 5 " model vdw 1.541 1.850 ... (remaining 492223 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: 0.860 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: 0.500 Extract box with map and model: 5.530 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 118.790 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.003 0.087 17899 Z= 0.199 Angle : 0.679 10.272 24248 Z= 0.369 Chirality : 0.043 0.272 2685 Planarity : 0.006 0.121 3046 Dihedral : 15.183 89.912 6991 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.69 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -2.68 (0.16), residues: 2111 helix: -0.99 (0.14), residues: 945 sheet: -2.70 (0.29), residues: 243 loop : -2.28 (0.17), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 537 HIS 0.004 0.001 HIS C 437 PHE 0.019 0.001 PHE C 323 TYR 0.023 0.001 TYR B 30 ARG 0.018 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 290 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 2.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 PHE cc_start: 0.6805 (m-10) cc_final: 0.6586 (m-10) REVERT: C 365 MET cc_start: 0.3947 (mpp) cc_final: 0.3454 (mtm) REVERT: C 402 MET cc_start: 0.3536 (mmp) cc_final: 0.2988 (mtt) REVERT: C 473 MET cc_start: 0.7354 (ttp) cc_final: 0.7098 (tmm) REVERT: C 475 MET cc_start: -0.1992 (mmm) cc_final: -0.3009 (mmm) REVERT: C 611 ASP cc_start: 0.7035 (m-30) cc_final: 0.6356 (m-30) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.8655 time to fit residues: 349.9241 Evaluate side-chains 186 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 9.9990 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 191 optimal weight: 0.0980 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17899 Z= 0.219 Angle : 0.556 6.946 24248 Z= 0.297 Chirality : 0.039 0.344 2685 Planarity : 0.005 0.071 3046 Dihedral : 9.555 73.287 2670 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 0.85 % Allowed : 5.74 % Favored : 93.41 % 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: -1.09 (0.17), residues: 2111 helix: 0.64 (0.16), residues: 953 sheet: -2.08 (0.30), residues: 252 loop : -1.78 (0.19), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 537 HIS 0.006 0.001 HIS B 562 PHE 0.028 0.001 PHE A 4 TYR 0.015 0.001 TYR B 555 ARG 0.007 0.001 ARG B 680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 3.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 365 MET cc_start: 0.4009 (mpp) cc_final: 0.3417 (mtm) REVERT: C 402 MET cc_start: 0.3608 (mmp) cc_final: 0.2994 (mtt) REVERT: C 473 MET cc_start: 0.7255 (ttp) cc_final: 0.7040 (tmm) REVERT: C 475 MET cc_start: -0.1522 (mmm) cc_final: -0.2347 (mmm) REVERT: C 646 ARG cc_start: 0.7513 (ppt170) cc_final: 0.7258 (ppt170) outliers start: 16 outliers final: 7 residues processed: 201 average time/residue: 0.7860 time to fit residues: 229.4283 Evaluate side-chains 181 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 174 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain C residue 536 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 190 optimal weight: 50.0000 chunk 65 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17899 Z= 0.364 Angle : 0.573 7.626 24248 Z= 0.310 Chirality : 0.040 0.348 2685 Planarity : 0.004 0.051 3046 Dihedral : 9.655 74.175 2670 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.46 % Favored : 96.49 % Rotamer: Outliers : 0.85 % Allowed : 6.96 % Favored : 92.19 % 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: -0.73 (0.18), residues: 2111 helix: 0.90 (0.17), residues: 961 sheet: -1.62 (0.32), residues: 234 loop : -1.68 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 537 HIS 0.007 0.001 HIS B 562 PHE 0.020 0.001 PHE C 580 TYR 0.014 0.002 TYR B 555 ARG 0.009 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 642 ASN cc_start: 0.5175 (m-40) cc_final: 0.3618 (m-40) REVERT: C 325 PHE cc_start: 0.6381 (t80) cc_final: 0.6134 (t80) REVERT: C 402 MET cc_start: 0.3667 (mmp) cc_final: 0.3050 (mtt) REVERT: C 475 MET cc_start: -0.1602 (mmm) cc_final: -0.2304 (mmm) REVERT: C 646 ARG cc_start: 0.7546 (ppt170) cc_final: 0.7336 (ppt170) outliers start: 16 outliers final: 9 residues processed: 184 average time/residue: 0.7650 time to fit residues: 206.4841 Evaluate side-chains 168 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 159 time to evaluate : 2.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 636 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 189 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 192 optimal weight: 8.9990 chunk 203 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 182 optimal weight: 30.0000 chunk 54 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17899 Z= 0.226 Angle : 0.511 6.763 24248 Z= 0.271 Chirality : 0.038 0.358 2685 Planarity : 0.004 0.044 3046 Dihedral : 9.549 73.688 2670 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 0.64 % Allowed : 7.92 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.18), residues: 2111 helix: 1.19 (0.17), residues: 957 sheet: -1.32 (0.32), residues: 232 loop : -1.48 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 537 HIS 0.004 0.001 HIS B 562 PHE 0.017 0.001 PHE A 105 TYR 0.012 0.001 TYR B 555 ARG 0.004 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 365 MET cc_start: 0.4337 (mpp) cc_final: 0.3556 (mtm) REVERT: C 402 MET cc_start: 0.3660 (mmp) cc_final: 0.3026 (mtt) REVERT: C 475 MET cc_start: -0.1977 (mmm) cc_final: -0.2540 (mmm) REVERT: C 646 ARG cc_start: 0.7598 (ppt170) cc_final: 0.7383 (ppt170) outliers start: 12 outliers final: 10 residues processed: 172 average time/residue: 0.7179 time to fit residues: 184.2227 Evaluate side-chains 167 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 157 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 575 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 169 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 183 optimal weight: 50.0000 chunk 51 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 17899 Z= 0.457 Angle : 0.587 7.159 24248 Z= 0.318 Chirality : 0.041 0.361 2685 Planarity : 0.004 0.040 3046 Dihedral : 9.659 76.842 2670 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 0.80 % Allowed : 8.87 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2111 helix: 1.06 (0.17), residues: 953 sheet: -1.23 (0.33), residues: 222 loop : -1.55 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 49 HIS 0.007 0.001 HIS B 562 PHE 0.015 0.001 PHE A 105 TYR 0.014 0.002 TYR B 555 ARG 0.004 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 365 MET cc_start: 0.4497 (mpp) cc_final: 0.3726 (mtm) REVERT: C 402 MET cc_start: 0.3632 (mmp) cc_final: 0.2960 (mtt) REVERT: C 475 MET cc_start: -0.1866 (mmm) cc_final: -0.2570 (mmm) REVERT: C 570 MET cc_start: 0.6703 (tpp) cc_final: 0.6454 (tpp) REVERT: C 646 ARG cc_start: 0.7618 (ppt170) cc_final: 0.7396 (ppt170) REVERT: C 675 LEU cc_start: 0.8278 (tt) cc_final: 0.8060 (mp) outliers start: 15 outliers final: 11 residues processed: 176 average time/residue: 0.7003 time to fit residues: 184.2242 Evaluate side-chains 170 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 546 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 68 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 169 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 30.0000 chunk 67 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17899 Z= 0.263 Angle : 0.520 11.401 24248 Z= 0.276 Chirality : 0.039 0.363 2685 Planarity : 0.004 0.038 3046 Dihedral : 9.573 77.875 2670 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.12 % Favored : 95.83 % Rotamer: Outliers : 0.85 % Allowed : 9.72 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2111 helix: 1.26 (0.17), residues: 953 sheet: -1.11 (0.33), residues: 232 loop : -1.40 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 537 HIS 0.004 0.001 HIS C 151 PHE 0.014 0.001 PHE A 148 TYR 0.011 0.001 TYR B 555 ARG 0.003 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 365 MET cc_start: 0.4453 (mpp) cc_final: 0.3687 (mtm) REVERT: C 402 MET cc_start: 0.3692 (mmp) cc_final: 0.3038 (mtt) REVERT: C 475 MET cc_start: -0.1751 (mmm) cc_final: -0.2403 (mmm) REVERT: C 570 MET cc_start: 0.6789 (tpp) cc_final: 0.6582 (tpp) REVERT: C 646 ARG cc_start: 0.7598 (ppt170) cc_final: 0.7366 (ppt170) REVERT: C 675 LEU cc_start: 0.8300 (tt) cc_final: 0.8069 (mp) outliers start: 16 outliers final: 13 residues processed: 169 average time/residue: 0.7067 time to fit residues: 178.1217 Evaluate side-chains 168 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 2.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 546 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 196 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 203 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17899 Z= 0.208 Angle : 0.498 10.025 24248 Z= 0.261 Chirality : 0.038 0.360 2685 Planarity : 0.004 0.037 3046 Dihedral : 9.474 79.080 2670 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 0.64 % Allowed : 10.10 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2111 helix: 1.46 (0.17), residues: 957 sheet: -0.97 (0.34), residues: 232 loop : -1.28 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 537 HIS 0.006 0.001 HIS B 562 PHE 0.016 0.001 PHE C 438 TYR 0.011 0.001 TYR B 555 ARG 0.004 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 365 MET cc_start: 0.4491 (mpp) cc_final: 0.3898 (mtm) REVERT: C 402 MET cc_start: 0.3774 (mmp) cc_final: 0.3134 (mtt) REVERT: C 475 MET cc_start: -0.2000 (mmm) cc_final: -0.2561 (mmm) REVERT: C 570 MET cc_start: 0.6882 (tpp) cc_final: 0.6653 (tpp) REVERT: C 675 LEU cc_start: 0.8236 (tt) cc_final: 0.7999 (mp) outliers start: 12 outliers final: 11 residues processed: 168 average time/residue: 0.7020 time to fit residues: 176.9457 Evaluate side-chains 168 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 546 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 125 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 184 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 182 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17899 Z= 0.347 Angle : 0.548 13.993 24248 Z= 0.292 Chirality : 0.039 0.362 2685 Planarity : 0.004 0.039 3046 Dihedral : 9.552 81.574 2670 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer: Outliers : 0.58 % Allowed : 10.57 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2111 helix: 1.26 (0.17), residues: 961 sheet: -0.96 (0.34), residues: 232 loop : -1.38 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 537 HIS 0.005 0.001 HIS B 562 PHE 0.020 0.001 PHE C 438 TYR 0.013 0.001 TYR B 555 ARG 0.005 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 343 MET cc_start: 0.8341 (mtt) cc_final: 0.8118 (mtt) REVERT: C 365 MET cc_start: 0.4681 (mpp) cc_final: 0.4339 (mtm) REVERT: C 402 MET cc_start: 0.3899 (mmp) cc_final: 0.3295 (mtt) REVERT: C 475 MET cc_start: -0.2098 (mmm) cc_final: -0.2643 (mmm) REVERT: C 646 ARG cc_start: 0.7608 (ppt170) cc_final: 0.7350 (ppt170) REVERT: C 675 LEU cc_start: 0.8261 (tt) cc_final: 0.8013 (mp) outliers start: 11 outliers final: 11 residues processed: 167 average time/residue: 0.6879 time to fit residues: 172.8446 Evaluate side-chains 166 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 155 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 546 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 194 optimal weight: 9.9990 chunk 177 optimal weight: 0.0370 chunk 189 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 188 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17899 Z= 0.156 Angle : 0.502 14.829 24248 Z= 0.260 Chirality : 0.038 0.361 2685 Planarity : 0.004 0.036 3046 Dihedral : 9.444 80.635 2670 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 0.43 % Allowed : 10.89 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.18), residues: 2111 helix: 1.52 (0.17), residues: 968 sheet: -0.71 (0.36), residues: 217 loop : -1.25 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 537 HIS 0.006 0.001 HIS C 437 PHE 0.021 0.001 PHE C 438 TYR 0.010 0.001 TYR B 217 ARG 0.005 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 159 time to evaluate : 3.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 365 MET cc_start: 0.4653 (mpp) cc_final: 0.4205 (mtm) REVERT: C 402 MET cc_start: 0.3883 (mmp) cc_final: 0.3272 (mtt) REVERT: C 475 MET cc_start: -0.2138 (mmm) cc_final: -0.2657 (mmm) REVERT: C 646 ARG cc_start: 0.7583 (ppt170) cc_final: 0.7315 (ppt170) REVERT: C 675 LEU cc_start: 0.8273 (tt) cc_final: 0.8018 (mp) outliers start: 8 outliers final: 8 residues processed: 164 average time/residue: 0.6760 time to fit residues: 168.8064 Evaluate side-chains 160 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 152 time to evaluate : 2.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 200 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 193 optimal weight: 20.0000 chunk 167 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN C 236 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17899 Z= 0.136 Angle : 0.489 13.383 24248 Z= 0.251 Chirality : 0.037 0.361 2685 Planarity : 0.003 0.036 3046 Dihedral : 9.354 78.904 2670 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 0.37 % Allowed : 10.89 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 2111 helix: 1.73 (0.17), residues: 971 sheet: -0.61 (0.36), residues: 216 loop : -1.13 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 619 HIS 0.005 0.001 HIS C 437 PHE 0.024 0.001 PHE C 438 TYR 0.010 0.001 TYR B 555 ARG 0.005 0.000 ARG C 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4222 Ramachandran restraints generated. 2111 Oldfield, 0 Emsley, 2111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 365 MET cc_start: 0.4648 (mpp) cc_final: 0.4108 (mtm) REVERT: C 402 MET cc_start: 0.3890 (mmp) cc_final: 0.3263 (mtt) REVERT: C 475 MET cc_start: -0.2054 (mmm) cc_final: -0.2487 (mmm) REVERT: C 675 LEU cc_start: 0.8213 (tt) cc_final: 0.7949 (mp) outliers start: 7 outliers final: 6 residues processed: 157 average time/residue: 0.6762 time to fit residues: 161.1593 Evaluate side-chains 154 residues out of total 1882 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 519 ASN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 536 MET Chi-restraints excluded: chain C residue 546 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.098817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.065288 restraints weight = 130770.053| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.23 r_work: 0.2942 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17899 Z= 0.227 Angle : 0.509 15.391 24248 Z= 0.264 Chirality : 0.038 0.359 2685 Planarity : 0.004 0.037 3046 Dihedral : 9.340 78.469 2670 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 0.43 % Allowed : 11.16 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 2111 helix: 1.72 (0.17), residues: 969 sheet: -0.61 (0.37), residues: 216 loop : -1.17 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 537 HIS 0.005 0.001 HIS C 437 PHE 0.021 0.001 PHE C 438 TYR 0.017 0.001 TYR B 436 ARG 0.005 0.000 ARG C 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6651.57 seconds wall clock time: 118 minutes 19.84 seconds (7099.84 seconds total)