Starting phenix.real_space_refine on Mon Aug 5 00:51:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r23_18834/08_2024/8r23_18834.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r23_18834/08_2024/8r23_18834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r23_18834/08_2024/8r23_18834.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r23_18834/08_2024/8r23_18834.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r23_18834/08_2024/8r23_18834.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r23_18834/08_2024/8r23_18834.cif" } resolution = 3.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 94 5.16 5 C 7660 2.51 5 N 2015 2.21 5 O 2208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 25": "OD1" <-> "OD2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ASP 142": "OD1" <-> "OD2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A ASP 622": "OD1" <-> "OD2" Residue "A GLU 656": "OE1" <-> "OE2" Residue "A GLU 690": "OE1" <-> "OE2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B ASP 92": "OD1" <-> "OD2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 386": "OD1" <-> "OD2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 401": "NH1" <-> "NH2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B ASP 491": "OD1" <-> "OD2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ASP 41": "OD1" <-> "OD2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ASP 106": "OD1" <-> "OD2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C GLU 421": "OE1" <-> "OE2" Residue "C TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 11979 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5468 Classifications: {'peptide': 718} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 674} Chain breaks: 9 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3128 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 370} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3381 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 410} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5455 SG CYS A 820 59.662 42.201 71.145 1.00 42.52 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N PRO A 492 " occ=0.25 ... (5 atoms not shown) pdb=" CD PRO A 492 " occ=0.25 Time building chain proxies: 6.97, per 1000 atoms: 0.58 Number of scatterers: 11979 At special positions: 0 Unit cell: (130.68, 109.56, 116.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 94 16.00 O 2208 8.00 N 2015 7.00 C 7660 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: 4.40 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 800 " pdb="ZN ZN C 800 " - pdb=" ND1 HIS C 70 " pdb="ZN ZN C 800 " - pdb=" NE2 HIS C 68 " pdb="ZN ZN C 800 " - pdb=" NE2 HIS C 157 " pdb=" ZN C 801 " pdb="ZN ZN C 801 " - pdb=" NE2 HIS C 73 " pdb="ZN ZN C 801 " - pdb=" NE2 HIS C 414 " pdb="ZN ZN C 801 " - pdb=" SG CYS A 820 " 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2908 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 43.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 3 through 6 No H-bonds generated for 'chain 'A' and resid 3 through 6' Processing helix chain 'A' and resid 9 through 17 removed outlier: 3.756A pdb=" N VAL A 17 " --> pdb=" O CYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 42 removed outlier: 3.750A pdb=" N TRP A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.505A pdb=" N GLN A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 62 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 99 through 102 No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.802A pdb=" N SER A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 142 Processing helix chain 'A' and resid 146 through 152 removed outlier: 3.849A pdb=" N SER A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 175 removed outlier: 3.696A pdb=" N ALA A 163 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 206 removed outlier: 3.777A pdb=" N LYS A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 227 removed outlier: 3.540A pdb=" N VAL A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLY A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.558A pdb=" N ALA A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Proline residue: A 242 - end of helix Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 270 through 273 No H-bonds generated for 'chain 'A' and resid 270 through 273' Processing helix chain 'A' and resid 278 through 289 removed outlier: 3.542A pdb=" N THR A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.617A pdb=" N LEU A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 320 removed outlier: 3.693A pdb=" N GLN A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 329 removed outlier: 3.671A pdb=" N VAL A 327 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 356 removed outlier: 3.789A pdb=" N THR A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'A' and resid 387 through 402 removed outlier: 3.652A pdb=" N VAL A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 419 removed outlier: 3.905A pdb=" N GLY A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 Processing helix chain 'A' and resid 443 through 457 removed outlier: 3.674A pdb=" N VAL A 452 " --> pdb=" O GLN A 448 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 478 removed outlier: 3.734A pdb=" N LEU A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 508 removed outlier: 3.513A pdb=" N ARG A 499 " --> pdb=" O PRO A 495 " (cutoff:3.500A) Proline residue: A 503 - end of helix removed outlier: 3.940A pdb=" N LYS A 507 " --> pdb=" O PRO A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 530 removed outlier: 3.635A pdb=" N LEU A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 Processing helix chain 'A' and resid 546 through 549 No H-bonds generated for 'chain 'A' and resid 546 through 549' Processing helix chain 'A' and resid 559 through 574 Processing helix chain 'A' and resid 593 through 601 removed outlier: 3.566A pdb=" N HIS A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 622 removed outlier: 3.622A pdb=" N GLN A 614 " --> pdb=" O ARG A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 643 removed outlier: 3.648A pdb=" N GLN A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 641 " --> pdb=" O THR A 637 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 665 removed outlier: 3.557A pdb=" N GLN A 664 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 665 " --> pdb=" O PHE A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'A' and resid 700 through 708 removed outlier: 3.534A pdb=" N CYS A 706 " --> pdb=" O ASP A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 732 removed outlier: 3.720A pdb=" N LYS A 718 " --> pdb=" O PRO A 714 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 729 " --> pdb=" O PHE A 725 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA A 731 " --> pdb=" O ARG A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 778 Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 799 through 807 removed outlier: 3.721A pdb=" N MET A 806 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 Processing helix chain 'B' and resid 127 through 144 removed outlier: 3.880A pdb=" N LEU B 135 " --> pdb=" O GLN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 190 removed outlier: 3.692A pdb=" N ASN B 188 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER B 189 " --> pdb=" O GLN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 304 through 319 removed outlier: 3.506A pdb=" N GLN B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 454 through 464 removed outlier: 3.549A pdb=" N SER B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 476 No H-bonds generated for 'chain 'B' and resid 473 through 476' Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 71 through 74 No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 77 through 80 No H-bonds generated for 'chain 'C' and resid 77 through 80' Processing helix chain 'C' and resid 94 through 111 removed outlier: 3.568A pdb=" N ALA C 98 " --> pdb=" O HIS C 94 " (cutoff:3.500A) Proline residue: C 101 - end of helix removed outlier: 3.689A pdb=" N LYS C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 removed outlier: 3.670A pdb=" N LYS C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 229 removed outlier: 3.655A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 257 removed outlier: 3.948A pdb=" N LEU C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 332 through 339 Processing helix chain 'C' and resid 359 through 364 removed outlier: 3.714A pdb=" N LEU C 364 " --> pdb=" O GLY C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 405 Processing helix chain 'C' and resid 417 through 429 removed outlier: 3.829A pdb=" N GLU C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 426 " --> pdb=" O PHE C 422 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1044 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: 2.90 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3870 1.34 - 1.46: 1747 1.46 - 1.57: 6482 1.57 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 12235 Sorted by residual: bond pdb=" N ASP A 251 " pdb=" CA ASP A 251 " ideal model delta sigma weight residual 1.463 1.456 0.007 6.90e-03 2.10e+04 1.07e+00 bond pdb=" C VAL A 795 " pdb=" O VAL A 795 " ideal model delta sigma weight residual 1.231 1.242 -0.010 1.02e-02 9.61e+03 1.02e+00 bond pdb=" CA CYS A 246 " pdb=" C CYS A 246 " ideal model delta sigma weight residual 1.523 1.505 0.018 1.80e-02 3.09e+03 9.78e-01 bond pdb=" CG LEU A 300 " pdb=" CD1 LEU A 300 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 9.01e-01 bond pdb=" CG PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.84e-01 ... (remaining 12230 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.08: 386 106.08 - 113.06: 6750 113.06 - 120.04: 4130 120.04 - 127.02: 5189 127.02 - 134.00: 166 Bond angle restraints: 16621 Sorted by residual: angle pdb=" N THR C 324 " pdb=" CA THR C 324 " pdb=" C THR C 324 " ideal model delta sigma weight residual 109.81 117.50 -7.69 2.21e+00 2.05e-01 1.21e+01 angle pdb=" N ALA A 115 " pdb=" CA ALA A 115 " pdb=" C ALA A 115 " ideal model delta sigma weight residual 114.75 110.68 4.07 1.26e+00 6.30e-01 1.04e+01 angle pdb=" N VAL A 397 " pdb=" CA VAL A 397 " pdb=" C VAL A 397 " ideal model delta sigma weight residual 113.43 109.92 3.51 1.09e+00 8.42e-01 1.04e+01 angle pdb=" N ASP A 251 " pdb=" CA ASP A 251 " pdb=" C ASP A 251 " ideal model delta sigma weight residual 112.17 108.22 3.95 1.36e+00 5.41e-01 8.42e+00 angle pdb=" N GLU B 145 " pdb=" CA GLU B 145 " pdb=" C GLU B 145 " ideal model delta sigma weight residual 110.65 107.13 3.52 1.26e+00 6.30e-01 7.78e+00 ... (remaining 16616 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6598 17.81 - 35.62: 641 35.62 - 53.44: 93 53.44 - 71.25: 25 71.25 - 89.06: 10 Dihedral angle restraints: 7367 sinusoidal: 2892 harmonic: 4475 Sorted by residual: dihedral pdb=" CA THR C 324 " pdb=" C THR C 324 " pdb=" N PRO C 325 " pdb=" CA PRO C 325 " ideal model delta harmonic sigma weight residual 180.00 156.02 23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ILE C 24 " pdb=" C ILE C 24 " pdb=" N ALA C 25 " pdb=" CA ALA C 25 " ideal model delta harmonic sigma weight residual -180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA GLY C 366 " pdb=" C GLY C 366 " pdb=" N GLN C 367 " pdb=" CA GLN C 367 " ideal model delta harmonic sigma weight residual 180.00 -161.27 -18.73 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 7364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1416 0.041 - 0.082: 382 0.082 - 0.122: 121 0.122 - 0.163: 11 0.163 - 0.204: 1 Chirality restraints: 1931 Sorted by residual: chirality pdb=" CB ILE B 490 " pdb=" CA ILE B 490 " pdb=" CG1 ILE B 490 " pdb=" CG2 ILE B 490 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA THR C 324 " pdb=" N THR C 324 " pdb=" C THR C 324 " pdb=" CB THR C 324 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CB ILE C 24 " pdb=" CA ILE C 24 " pdb=" CG1 ILE C 24 " pdb=" CG2 ILE C 24 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 1928 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 324 " -0.060 5.00e-02 4.00e+02 9.00e-02 1.30e+01 pdb=" N PRO C 325 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO C 325 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 325 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 105 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO A 106 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 556 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO A 557 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 557 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 557 " -0.028 5.00e-02 4.00e+02 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 80 2.56 - 3.15: 9748 3.15 - 3.73: 17243 3.73 - 4.32: 24987 4.32 - 4.90: 41178 Nonbonded interactions: 93236 Sorted by model distance: nonbonded pdb=" OD2 ASP C 178 " pdb="ZN ZN C 800 " model vdw 1.978 2.230 nonbonded pdb=" OD2 ASP C 72 " pdb="ZN ZN C 801 " model vdw 2.047 2.230 nonbonded pdb=" OH TYR B 112 " pdb=" O ARG B 180 " model vdw 2.170 3.040 nonbonded pdb=" O ASP A 556 " pdb=" NH1 ARG A 562 " model vdw 2.211 3.120 nonbonded pdb=" O TRP A 237 " pdb=" OG SER A 241 " model vdw 2.219 3.040 ... (remaining 93231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 35.140 Find NCS groups from input model: 0.130 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12235 Z= 0.284 Angle : 0.661 7.693 16621 Z= 0.372 Chirality : 0.041 0.204 1931 Planarity : 0.005 0.090 2118 Dihedral : 14.388 89.059 4459 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -5.33 (0.16), residues: 1508 helix: -3.39 (0.13), residues: 768 sheet: -3.29 (0.34), residues: 179 loop : -3.55 (0.21), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 114 HIS 0.005 0.001 HIS A 294 PHE 0.017 0.001 PHE C 312 TYR 0.013 0.001 TYR C 278 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7198 (mtp) cc_final: 0.6967 (mtp) REVERT: A 199 MET cc_start: 0.7790 (mtt) cc_final: 0.7165 (mtt) REVERT: A 458 GLU cc_start: 0.7817 (pp20) cc_final: 0.7194 (pp20) REVERT: A 718 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8376 (mmtp) REVERT: B 32 MET cc_start: 0.6886 (mmp) cc_final: 0.6148 (tpp) REVERT: B 464 VAL cc_start: 0.8334 (t) cc_final: 0.8102 (m) REVERT: C 143 GLN cc_start: 0.7985 (tp-100) cc_final: 0.6987 (mm110) REVERT: C 149 GLU cc_start: 0.6840 (mt-10) cc_final: 0.5884 (mm-30) REVERT: C 259 MET cc_start: 0.8041 (mmm) cc_final: 0.7653 (mmt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2895 time to fit residues: 74.5344 Evaluate side-chains 123 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.0170 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 GLN A 472 GLN A 506 GLN A 767 GLN A 800 GLN A 804 GLN B 224 ASN B 456 GLN B 493 GLN C 124 GLN C 143 GLN C 277 HIS C 332 GLN C 343 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12235 Z= 0.192 Angle : 0.579 6.383 16621 Z= 0.289 Chirality : 0.041 0.153 1931 Planarity : 0.005 0.087 2118 Dihedral : 4.508 42.729 1633 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.36 % Allowed : 9.50 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -3.16 (0.20), residues: 1508 helix: -1.46 (0.17), residues: 786 sheet: -2.53 (0.40), residues: 155 loop : -2.74 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 385 HIS 0.006 0.001 HIS B 484 PHE 0.014 0.001 PHE C 312 TYR 0.017 0.001 TYR C 278 ARG 0.005 0.000 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7222 (mtp) cc_final: 0.6990 (mtp) REVERT: A 261 ASP cc_start: 0.7774 (m-30) cc_final: 0.7373 (m-30) REVERT: A 396 THR cc_start: 0.9408 (t) cc_final: 0.9155 (m) REVERT: A 458 GLU cc_start: 0.7944 (pp20) cc_final: 0.7306 (pp20) REVERT: A 692 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8674 (tp) REVERT: A 718 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8315 (mmtp) REVERT: B 489 MET cc_start: 0.8217 (ttp) cc_final: 0.7848 (ttp) REVERT: C 106 ASP cc_start: 0.7681 (t0) cc_final: 0.7451 (t70) REVERT: C 138 LEU cc_start: 0.8505 (mp) cc_final: 0.8284 (mp) REVERT: C 149 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6100 (mt-10) REVERT: C 259 MET cc_start: 0.7977 (mmm) cc_final: 0.7698 (mmp) REVERT: C 430 GLU cc_start: 0.7462 (tm-30) cc_final: 0.7235 (tm-30) outliers start: 18 outliers final: 9 residues processed: 160 average time/residue: 0.2568 time to fit residues: 58.3929 Evaluate side-chains 132 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 219 ARG Chi-restraints excluded: chain C residue 347 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 0.0970 chunk 150 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 47 optimal weight: 0.0060 chunk 111 optimal weight: 0.0050 overall best weight: 0.3008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN A 800 GLN A 804 GLN B 407 HIS ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12235 Z= 0.151 Angle : 0.530 9.067 16621 Z= 0.262 Chirality : 0.040 0.153 1931 Planarity : 0.005 0.076 2118 Dihedral : 4.054 36.895 1633 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.13 % Allowed : 11.83 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -1.93 (0.21), residues: 1508 helix: -0.34 (0.19), residues: 787 sheet: -2.03 (0.43), residues: 139 loop : -2.34 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 385 HIS 0.005 0.001 HIS B 484 PHE 0.024 0.001 PHE C 282 TYR 0.018 0.001 TYR C 107 ARG 0.003 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 1.387 Fit side-chains REVERT: A 261 ASP cc_start: 0.7579 (m-30) cc_final: 0.7185 (m-30) REVERT: A 396 THR cc_start: 0.9395 (t) cc_final: 0.9112 (m) REVERT: A 458 GLU cc_start: 0.7961 (pp20) cc_final: 0.7297 (pp20) REVERT: A 522 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7336 (mm-30) REVERT: A 644 ARG cc_start: 0.7643 (mmp80) cc_final: 0.7423 (mmm160) REVERT: A 692 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8668 (tp) REVERT: A 708 LEU cc_start: 0.8486 (tp) cc_final: 0.8251 (tp) REVERT: B 250 MET cc_start: 0.6351 (tpt) cc_final: 0.5992 (tpt) REVERT: B 489 MET cc_start: 0.8139 (ttp) cc_final: 0.7762 (ttp) REVERT: C 106 ASP cc_start: 0.7427 (t0) cc_final: 0.7197 (t70) REVERT: C 138 LEU cc_start: 0.8442 (mp) cc_final: 0.8242 (mp) outliers start: 15 outliers final: 8 residues processed: 144 average time/residue: 0.2339 time to fit residues: 49.5824 Evaluate side-chains 125 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 446 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 93 optimal weight: 0.0970 chunk 139 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN C 260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12235 Z= 0.319 Angle : 0.589 7.817 16621 Z= 0.292 Chirality : 0.043 0.168 1931 Planarity : 0.005 0.081 2118 Dihedral : 4.286 38.417 1633 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.51 % Allowed : 13.19 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.22), residues: 1508 helix: -0.09 (0.19), residues: 789 sheet: -2.16 (0.41), residues: 153 loop : -2.27 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 285 HIS 0.004 0.001 HIS A 294 PHE 0.022 0.002 PHE C 282 TYR 0.021 0.001 TYR C 107 ARG 0.005 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 1.253 Fit side-chains REVERT: A 396 THR cc_start: 0.9447 (t) cc_final: 0.9132 (m) REVERT: A 458 GLU cc_start: 0.8023 (pp20) cc_final: 0.7426 (pp20) REVERT: A 718 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8362 (mmtp) REVERT: B 250 MET cc_start: 0.6567 (tpt) cc_final: 0.6235 (tpt) outliers start: 20 outliers final: 16 residues processed: 133 average time/residue: 0.2341 time to fit residues: 45.3979 Evaluate side-chains 127 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 446 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12235 Z= 0.265 Angle : 0.563 7.330 16621 Z= 0.278 Chirality : 0.042 0.151 1931 Planarity : 0.005 0.080 2118 Dihedral : 4.264 37.892 1633 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.81 % Allowed : 14.62 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -1.43 (0.22), residues: 1508 helix: 0.14 (0.19), residues: 787 sheet: -2.04 (0.42), residues: 153 loop : -2.12 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 191 HIS 0.004 0.001 HIS A 294 PHE 0.018 0.001 PHE C 282 TYR 0.020 0.001 TYR C 107 ARG 0.004 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.456 Fit side-chains REVERT: A 396 THR cc_start: 0.9500 (t) cc_final: 0.9181 (m) REVERT: A 458 GLU cc_start: 0.8048 (pp20) cc_final: 0.7463 (pp20) REVERT: A 718 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8352 (mmtp) REVERT: B 250 MET cc_start: 0.6586 (tpt) cc_final: 0.6331 (tpt) REVERT: B 489 MET cc_start: 0.8184 (ttp) cc_final: 0.7906 (ttp) outliers start: 24 outliers final: 19 residues processed: 140 average time/residue: 0.2279 time to fit residues: 47.7421 Evaluate side-chains 132 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 446 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 0.0040 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12235 Z= 0.188 Angle : 0.529 7.165 16621 Z= 0.262 Chirality : 0.041 0.147 1931 Planarity : 0.005 0.073 2118 Dihedral : 4.060 35.425 1633 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.73 % Allowed : 15.37 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -1.04 (0.22), residues: 1508 helix: 0.43 (0.19), residues: 793 sheet: -1.56 (0.45), residues: 143 loop : -2.02 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 385 HIS 0.003 0.001 HIS A 294 PHE 0.016 0.001 PHE C 422 TYR 0.019 0.001 TYR C 107 ARG 0.004 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.436 Fit side-chains REVERT: A 261 ASP cc_start: 0.7693 (m-30) cc_final: 0.7249 (m-30) REVERT: A 396 THR cc_start: 0.9484 (t) cc_final: 0.9164 (m) REVERT: A 458 GLU cc_start: 0.8057 (pp20) cc_final: 0.7504 (pp20) REVERT: A 708 LEU cc_start: 0.8588 (tp) cc_final: 0.8321 (tp) REVERT: B 32 MET cc_start: 0.5937 (mmp) cc_final: 0.4908 (mmm) REVERT: B 489 MET cc_start: 0.8184 (ttp) cc_final: 0.7872 (ttp) outliers start: 23 outliers final: 18 residues processed: 138 average time/residue: 0.2220 time to fit residues: 45.6768 Evaluate side-chains 130 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 446 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 0.1980 chunk 84 optimal weight: 0.0970 chunk 108 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12235 Z= 0.204 Angle : 0.539 7.831 16621 Z= 0.267 Chirality : 0.041 0.178 1931 Planarity : 0.005 0.071 2118 Dihedral : 4.017 34.282 1633 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.88 % Allowed : 15.37 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.86 (0.22), residues: 1508 helix: 0.56 (0.19), residues: 794 sheet: -1.40 (0.45), residues: 143 loop : -1.93 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.005 0.001 HIS C 157 PHE 0.018 0.001 PHE C 422 TYR 0.018 0.001 TYR C 107 ARG 0.004 0.000 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 1.332 Fit side-chains REVERT: A 261 ASP cc_start: 0.7694 (m-30) cc_final: 0.7481 (m-30) REVERT: A 396 THR cc_start: 0.9483 (t) cc_final: 0.9160 (m) REVERT: A 458 GLU cc_start: 0.8057 (pp20) cc_final: 0.7530 (pp20) REVERT: A 708 LEU cc_start: 0.8571 (tp) cc_final: 0.8344 (tp) REVERT: B 32 MET cc_start: 0.6264 (mmp) cc_final: 0.5178 (mmm) REVERT: C 420 MET cc_start: 0.8454 (mtp) cc_final: 0.8179 (mtm) outliers start: 25 outliers final: 20 residues processed: 135 average time/residue: 0.2055 time to fit residues: 42.5037 Evaluate side-chains 127 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 446 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 0.0170 chunk 93 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 134 optimal weight: 0.0170 chunk 141 optimal weight: 0.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12235 Z= 0.163 Angle : 0.518 7.722 16621 Z= 0.256 Chirality : 0.040 0.197 1931 Planarity : 0.004 0.067 2118 Dihedral : 3.855 30.920 1633 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.81 % Allowed : 15.67 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1508 helix: 0.75 (0.19), residues: 796 sheet: -1.18 (0.46), residues: 143 loop : -1.82 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 191 HIS 0.003 0.001 HIS A 294 PHE 0.018 0.001 PHE C 422 TYR 0.024 0.001 TYR C 107 ARG 0.004 0.000 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 1.256 Fit side-chains REVERT: A 176 MET cc_start: 0.8382 (ptp) cc_final: 0.8149 (ptp) REVERT: A 261 ASP cc_start: 0.7659 (m-30) cc_final: 0.7215 (m-30) REVERT: A 302 ILE cc_start: 0.8799 (mm) cc_final: 0.8532 (mt) REVERT: A 396 THR cc_start: 0.9473 (t) cc_final: 0.9150 (m) REVERT: A 458 GLU cc_start: 0.8088 (pp20) cc_final: 0.7577 (pp20) REVERT: A 569 MET cc_start: 0.7778 (mmm) cc_final: 0.7576 (mmm) REVERT: A 644 ARG cc_start: 0.7693 (mmp80) cc_final: 0.7472 (tpp80) REVERT: A 692 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8676 (tp) REVERT: A 708 LEU cc_start: 0.8570 (tp) cc_final: 0.8362 (tp) REVERT: B 32 MET cc_start: 0.6126 (mmp) cc_final: 0.4999 (mmm) REVERT: B 137 MET cc_start: 0.8893 (mtt) cc_final: 0.8615 (mtt) REVERT: B 280 GLU cc_start: 0.7546 (tp30) cc_final: 0.7091 (tp30) REVERT: B 489 MET cc_start: 0.8254 (ttp) cc_final: 0.7968 (ttp) outliers start: 24 outliers final: 19 residues processed: 138 average time/residue: 0.2114 time to fit residues: 44.0124 Evaluate side-chains 133 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 446 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 90 optimal weight: 0.0470 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12235 Z= 0.215 Angle : 0.544 8.097 16621 Z= 0.267 Chirality : 0.041 0.206 1931 Planarity : 0.005 0.069 2118 Dihedral : 3.923 30.267 1633 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.66 % Allowed : 15.83 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.56 (0.23), residues: 1508 helix: 0.79 (0.19), residues: 796 sheet: -1.17 (0.46), residues: 143 loop : -1.82 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 191 HIS 0.004 0.001 HIS C 157 PHE 0.019 0.001 PHE C 422 TYR 0.021 0.001 TYR C 107 ARG 0.009 0.000 ARG B 500 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.446 Fit side-chains REVERT: A 261 ASP cc_start: 0.7695 (m-30) cc_final: 0.7494 (m-30) REVERT: A 396 THR cc_start: 0.9485 (t) cc_final: 0.9159 (m) REVERT: A 458 GLU cc_start: 0.8097 (pp20) cc_final: 0.7588 (pp20) REVERT: B 32 MET cc_start: 0.6223 (mmp) cc_final: 0.5139 (mmm) REVERT: B 280 GLU cc_start: 0.7545 (tp30) cc_final: 0.7131 (tp30) REVERT: B 489 MET cc_start: 0.8333 (ttp) cc_final: 0.7993 (ttp) REVERT: C 420 MET cc_start: 0.8369 (mtp) cc_final: 0.8086 (mtm) outliers start: 22 outliers final: 19 residues processed: 128 average time/residue: 0.2033 time to fit residues: 40.3061 Evaluate side-chains 128 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 493 GLN Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 3.9990 chunk 88 optimal weight: 0.0270 chunk 68 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 96 optimal weight: 0.2980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12235 Z= 0.151 Angle : 0.523 8.249 16621 Z= 0.257 Chirality : 0.040 0.214 1931 Planarity : 0.004 0.064 2118 Dihedral : 3.802 27.949 1633 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.43 % Allowed : 16.05 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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 (0.23), residues: 1508 helix: 0.94 (0.19), residues: 797 sheet: -0.97 (0.47), residues: 143 loop : -1.73 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 191 HIS 0.003 0.001 HIS A 294 PHE 0.018 0.001 PHE C 422 TYR 0.027 0.001 TYR C 107 ARG 0.008 0.000 ARG B 500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3016 Ramachandran restraints generated. 1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.325 Fit side-chains REVERT: A 261 ASP cc_start: 0.7665 (m-30) cc_final: 0.7239 (m-30) REVERT: A 302 ILE cc_start: 0.8844 (mm) cc_final: 0.8588 (mt) REVERT: A 396 THR cc_start: 0.9457 (t) cc_final: 0.9129 (m) REVERT: A 458 GLU cc_start: 0.8037 (pp20) cc_final: 0.7730 (pp20) REVERT: A 569 MET cc_start: 0.7778 (mmm) cc_final: 0.7557 (mmm) REVERT: A 644 ARG cc_start: 0.7730 (mmp80) cc_final: 0.7477 (tpp80) REVERT: A 692 LEU cc_start: 0.8901 (mp) cc_final: 0.8688 (tp) REVERT: A 708 LEU cc_start: 0.8547 (tp) cc_final: 0.8329 (tp) REVERT: B 32 MET cc_start: 0.6071 (mmp) cc_final: 0.4954 (mmm) REVERT: B 280 GLU cc_start: 0.7532 (tp30) cc_final: 0.7072 (tp30) REVERT: B 489 MET cc_start: 0.8284 (ttp) cc_final: 0.7985 (ttp) REVERT: C 420 MET cc_start: 0.8358 (mtp) cc_final: 0.8063 (mtm) outliers start: 19 outliers final: 19 residues processed: 131 average time/residue: 0.2243 time to fit residues: 45.4204 Evaluate side-chains 131 residues out of total 1333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 50 optimal weight: 0.0040 chunk 124 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.132493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.097117 restraints weight = 18864.805| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.51 r_work: 0.3037 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12235 Z= 0.175 Angle : 0.523 7.841 16621 Z= 0.256 Chirality : 0.041 0.212 1931 Planarity : 0.005 0.067 2118 Dihedral : 3.756 25.654 1633 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.66 % Allowed : 16.05 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -0.32 (0.23), residues: 1508 helix: 0.94 (0.19), residues: 804 sheet: -0.90 (0.47), residues: 143 loop : -1.71 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 191 HIS 0.003 0.001 HIS C 157 PHE 0.019 0.001 PHE C 422 TYR 0.027 0.001 TYR C 107 ARG 0.008 0.000 ARG B 500 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2416.22 seconds wall clock time: 43 minutes 52.02 seconds (2632.02 seconds total)