Starting phenix.real_space_refine on Mon Mar 18 06:51:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui7_26541/03_2024/7ui7_26541.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui7_26541/03_2024/7ui7_26541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui7_26541/03_2024/7ui7_26541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui7_26541/03_2024/7ui7_26541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui7_26541/03_2024/7ui7_26541.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ui7_26541/03_2024/7ui7_26541.pdb" } resolution = 3.4 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= 0.031 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 Mn 4 7.51 5 S 54 5.16 5 C 6606 2.51 5 N 1746 2.21 5 O 1804 1.98 5 H 10079 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 207": "OE1" <-> "OE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A ASP 507": "OD1" <-> "OD2" Residue "A PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A TYR 749": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 473": "OD1" <-> "OD2" Residue "B PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20293 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 10145 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 23, 'TRANS': 589} Chain breaks: 1 Chain: "B" Number of atoms: 10144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 10144 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 23, 'TRANS': 589} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.51, per 1000 atoms: 0.47 Number of scatterers: 20293 At special positions: 0 Unit cell: (115.416, 106.6, 104.195, 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) Mn 4 24.99 S 54 16.00 O 1804 8.00 N 1746 7.00 C 6606 6.00 H 10079 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 726 " distance=2.03 Simple disulfide: pdb=" SG CYS B 354 " - pdb=" SG CYS B 369 " distance=2.03 Simple disulfide: pdb=" SG CYS B 443 " - pdb=" SG CYS B 726 " distance=2.03 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: 16.33 Conformation dependent library (CDL) restraints added in 2.1 seconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 11 sheets defined 48.0% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.734A pdb=" N THR A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.764A pdb=" N VAL A 208 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 removed outlier: 3.517A pdb=" N LYS A 224 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 231 Processing helix chain 'A' and resid 250 through 256 removed outlier: 4.008A pdb=" N LEU A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 303 through 310 removed outlier: 3.590A pdb=" N LEU A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 333 through 344 removed outlier: 3.735A pdb=" N ASN A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.791A pdb=" N CYS A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.581A pdb=" N VAL A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 406 removed outlier: 3.864A pdb=" N PHE A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 427 through 435 Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.725A pdb=" N PHE A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 452 " --> pdb=" O ARG A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 486 removed outlier: 5.855A pdb=" N GLN A 486 " --> pdb=" O ASP A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 495 removed outlier: 3.614A pdb=" N HIS A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 520 removed outlier: 3.617A pdb=" N GLN A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 526 removed outlier: 3.631A pdb=" N ARG A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.847A pdb=" N HIS A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 584 Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.612A pdb=" N GLY A 633 " --> pdb=" O TRP A 630 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS A 634 " --> pdb=" O THR A 631 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 635 " --> pdb=" O LYS A 632 " (cutoff:3.500A) Proline residue: A 636 - end of helix No H-bonds generated for 'chain 'A' and resid 630 through 637' Processing helix chain 'A' and resid 638 through 644 removed outlier: 3.838A pdb=" N TRP A 642 " --> pdb=" O ASN A 638 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 691 removed outlier: 3.722A pdb=" N GLN A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 718 removed outlier: 3.723A pdb=" N THR A 715 " --> pdb=" O SER A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 743 removed outlier: 3.909A pdb=" N ARG A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 756 removed outlier: 3.810A pdb=" N LEU A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TYR A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 163 removed outlier: 4.215A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N HIS B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 190 removed outlier: 3.691A pdb=" N MET B 190 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.563A pdb=" N VAL B 208 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 250 through 257 removed outlier: 4.286A pdb=" N LEU B 254 " --> pdb=" O ASP B 250 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 303 through 310 Processing helix chain 'B' and resid 311 through 323 removed outlier: 4.035A pdb=" N MET B 315 " --> pdb=" O LYS B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 344 removed outlier: 3.522A pdb=" N ILE B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.648A pdb=" N ASN B 357 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.934A pdb=" N GLN B 368 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.959A pdb=" N VAL B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 406 removed outlier: 3.500A pdb=" N PHE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 427 through 437 removed outlier: 3.770A pdb=" N GLU B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 437 " --> pdb=" O GLN B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 451 removed outlier: 4.032A pdb=" N ARG B 447 " --> pdb=" O CYS B 443 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 485 Processing helix chain 'B' and resid 486 through 495 removed outlier: 4.163A pdb=" N ALA B 490 " --> pdb=" O GLN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 520 Processing helix chain 'B' and resid 520 through 526 Processing helix chain 'B' and resid 542 through 553 removed outlier: 3.876A pdb=" N HIS B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 584 Processing helix chain 'B' and resid 609 through 620 Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.680A pdb=" N HIS B 634 " --> pdb=" O THR B 631 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA B 635 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Proline residue: B 636 - end of helix Processing helix chain 'B' and resid 638 through 643 removed outlier: 3.664A pdb=" N TRP B 642 " --> pdb=" O ASN B 638 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 643 " --> pdb=" O PHE B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 638 through 643' Processing helix chain 'B' and resid 680 through 691 removed outlier: 4.147A pdb=" N HIS B 684 " --> pdb=" O ASN B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 720 removed outlier: 3.922A pdb=" N THR B 715 " --> pdb=" O SER B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 743 removed outlier: 3.690A pdb=" N ARG B 724 " --> pdb=" O ASN B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 756 removed outlier: 4.119A pdb=" N LEU B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 200 removed outlier: 6.688A pdb=" N LEU A 168 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP A 197 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE A 170 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N TYR A 199 " --> pdb=" O PHE A 170 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 172 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N HIS A 139 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU A 241 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA A 141 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL A 270 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY A 298 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 11.178A pdb=" N GLY A 268 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 247 removed outlier: 3.593A pdb=" N ILE A 379 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 456 through 457 removed outlier: 3.581A pdb=" N ILE A 533 " --> pdb=" O HIS A 457 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 530 removed outlier: 7.022A pdb=" N ILE A 499 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU A 476 " --> pdb=" O SER A 500 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 661 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARG A 664 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N LYS A 590 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 649 " --> pdb=" O VAL A 697 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 597 through 599 Processing sheet with id=AA6, first strand: chain 'B' and resid 194 through 200 removed outlier: 6.921A pdb=" N LEU B 168 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ASP B 197 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE B 170 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N TYR B 199 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B 172 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE B 138 " --> pdb=" O HIS B 169 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N HIS B 171 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 140 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE B 173 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE B 142 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N HIS B 139 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU B 241 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA B 141 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 247 removed outlier: 3.896A pdb=" N HIS B 380 " --> pdb=" O VAL B 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 269 through 270 removed outlier: 7.365A pdb=" N LEU B 269 " --> pdb=" O LEU B 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 456 through 457 Processing sheet with id=AB1, first strand: chain 'B' and resid 479 through 480 removed outlier: 4.073A pdb=" N LEU B 480 " --> pdb=" O ALA B 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 558 through 560 removed outlier: 5.103A pdb=" N ARG B 664 " --> pdb=" O LYS B 590 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N LYS B 590 " --> pdb=" O ARG B 664 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ALA B 591 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE B 695 " --> pdb=" O VAL B 651 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 649 " --> pdb=" O VAL B 697 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 933 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: 7.40 Time building geometry restraints manager: 17.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10071 1.03 - 1.23: 32 1.23 - 1.43: 4554 1.43 - 1.62: 5818 1.62 - 1.82: 92 Bond restraints: 20567 Sorted by residual: bond pdb=" C HIS A 705 " pdb=" N MET A 706 " ideal model delta sigma weight residual 1.332 1.359 -0.026 1.44e-02 4.82e+03 3.37e+00 bond pdb=" CB GLN B 691 " pdb=" CG GLN B 691 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.40e+00 bond pdb=" CA LYS A 224 " pdb=" C LYS A 224 " ideal model delta sigma weight residual 1.522 1.499 0.022 1.72e-02 3.38e+03 1.68e+00 bond pdb=" CB VAL A 682 " pdb=" CG1 VAL A 682 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.07e+00 bond pdb=" CG GLU B 321 " pdb=" CD GLU B 321 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 9.74e-01 ... (remaining 20562 not shown) Histogram of bond angle deviations from ideal: 97.90 - 105.13: 152 105.13 - 112.36: 22981 112.36 - 119.59: 5413 119.59 - 126.82: 8337 126.82 - 134.05: 187 Bond angle restraints: 37070 Sorted by residual: angle pdb=" CA GLN B 691 " pdb=" CB GLN B 691 " pdb=" CG GLN B 691 " ideal model delta sigma weight residual 114.10 122.00 -7.90 2.00e+00 2.50e-01 1.56e+01 angle pdb=" CB GLN B 691 " pdb=" CG GLN B 691 " pdb=" CD GLN B 691 " ideal model delta sigma weight residual 112.60 119.08 -6.48 1.70e+00 3.46e-01 1.45e+01 angle pdb=" C ALA B 320 " pdb=" N GLU B 321 " pdb=" CA GLU B 321 " ideal model delta sigma weight residual 120.31 115.56 4.75 1.52e+00 4.33e-01 9.78e+00 angle pdb=" N GLU B 321 " pdb=" CA GLU B 321 " pdb=" CB GLU B 321 " ideal model delta sigma weight residual 110.28 114.84 -4.56 1.55e+00 4.16e-01 8.66e+00 angle pdb=" N GLU A 732 " pdb=" CA GLU A 732 " pdb=" CB GLU A 732 " ideal model delta sigma weight residual 110.12 113.98 -3.86 1.47e+00 4.63e-01 6.89e+00 ... (remaining 37065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 8640 16.89 - 33.78: 779 33.78 - 50.67: 195 50.67 - 67.57: 58 67.57 - 84.46: 13 Dihedral angle restraints: 9685 sinusoidal: 5126 harmonic: 4559 Sorted by residual: dihedral pdb=" CB CYS A 443 " pdb=" SG CYS A 443 " pdb=" SG CYS A 726 " pdb=" CB CYS A 726 " ideal model delta sinusoidal sigma weight residual 93.00 134.40 -41.40 1 1.00e+01 1.00e-02 2.40e+01 dihedral pdb=" CA MET A 703 " pdb=" C MET A 703 " pdb=" N ILE A 704 " pdb=" CA ILE A 704 " ideal model delta harmonic sigma weight residual -180.00 -158.30 -21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA LYS A 432 " pdb=" C LYS A 432 " pdb=" N GLN A 433 " pdb=" CA GLN A 433 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 9682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1028 0.034 - 0.068: 358 0.068 - 0.102: 93 0.102 - 0.136: 43 0.136 - 0.170: 8 Chirality restraints: 1530 Sorted by residual: chirality pdb=" CA ILE A 300 " pdb=" N ILE A 300 " pdb=" C ILE A 300 " pdb=" CB ILE A 300 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA VAL B 662 " pdb=" N VAL B 662 " pdb=" C VAL B 662 " pdb=" CB VAL B 662 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA VAL A 662 " pdb=" N VAL A 662 " pdb=" C VAL A 662 " pdb=" CB VAL A 662 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 1527 not shown) Planarity restraints: 2972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 679 " 0.022 2.00e-02 2.50e+03 1.85e-02 1.37e+01 pdb=" CG TRP A 679 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 679 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 679 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 679 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP A 679 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 679 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 679 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 679 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 679 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP A 679 " 0.013 2.00e-02 2.50e+03 pdb=" HE1 TRP A 679 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 679 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 679 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 679 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 679 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 691 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C GLN B 691 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN B 691 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU B 692 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 567 " 0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO B 568 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 568 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 568 " 0.031 5.00e-02 4.00e+02 ... (remaining 2969 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 840 2.15 - 2.76: 39026 2.76 - 3.37: 57070 3.37 - 3.99: 71257 3.99 - 4.60: 111646 Nonbonded interactions: 279839 Sorted by model distance: nonbonded pdb=" OD1 ASN A 296 " pdb="HD22 ASN A 357 " model vdw 1.533 1.850 nonbonded pdb=" O GLU B 236 " pdb=" H LEU B 304 " model vdw 1.562 1.850 nonbonded pdb="HE22 GLN A 264 " pdb=" O PHE A 347 " model vdw 1.584 1.850 nonbonded pdb=" H ASN B 272 " pdb=" O GLY B 294 " model vdw 1.593 1.850 nonbonded pdb=" O SER B 206 " pdb=" HG SER B 209 " model vdw 1.604 1.850 ... (remaining 279834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 133 through 379 or (resid 380 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1)) or r \ esid 381 through 756 or resid 801 through 802)) selection = chain 'B' } 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: 1.450 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: 0.310 Extract box with map and model: 6.670 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 65.530 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 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 0.046 10488 Z= 0.250 Angle : 0.612 7.903 14218 Z= 0.339 Chirality : 0.041 0.170 1530 Planarity : 0.004 0.057 1796 Dihedral : 14.826 84.457 3852 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.23), residues: 1218 helix: -0.66 (0.24), residues: 414 sheet: -1.85 (0.41), residues: 138 loop : -1.41 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 679 HIS 0.022 0.001 HIS B 684 PHE 0.019 0.002 PHE B 625 TYR 0.016 0.002 TYR B 670 ARG 0.004 0.000 ARG B 740 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.508 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: 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 496 GLU cc_start: 0.6792 (tp30) cc_final: 0.6441 (tm-30) REVERT: A 528 ASN cc_start: 0.8026 (p0) cc_final: 0.7763 (p0) REVERT: A 574 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7446 (mm-30) REVERT: A 603 ARG cc_start: 0.7537 (mtt-85) cc_final: 0.7260 (mtt-85) REVERT: B 158 LYS cc_start: 0.7566 (mmmm) cc_final: 0.7167 (tttm) REVERT: B 187 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7893 (tm-30) REVERT: B 197 ASP cc_start: 0.7907 (m-30) cc_final: 0.7619 (m-30) REVERT: B 436 GLU cc_start: 0.7498 (pm20) cc_final: 0.7249 (mp0) REVERT: B 445 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7337 (mp0) REVERT: B 548 ASN cc_start: 0.7910 (p0) cc_final: 0.7599 (p0) REVERT: B 652 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6893 (mm-30) REVERT: B 654 GLU cc_start: 0.7671 (mp0) cc_final: 0.7214 (mp0) REVERT: B 656 ASP cc_start: 0.7405 (m-30) cc_final: 0.7125 (m-30) REVERT: B 658 GLU cc_start: 0.7509 (pt0) cc_final: 0.7275 (pt0) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.5796 time to fit residues: 223.6369 Evaluate side-chains 282 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN A 700 ASN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10488 Z= 0.222 Angle : 0.556 5.565 14218 Z= 0.297 Chirality : 0.040 0.175 1530 Planarity : 0.004 0.042 1796 Dihedral : 4.799 19.059 1364 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.99 % Favored : 93.92 % Rotamer: Outliers : 0.81 % Allowed : 6.06 % Favored : 93.13 % 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: -1.68 (0.23), residues: 1218 helix: -0.33 (0.25), residues: 434 sheet: -2.18 (0.38), residues: 160 loop : -1.32 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 679 HIS 0.006 0.001 HIS A 163 PHE 0.010 0.001 PHE A 513 TYR 0.013 0.001 TYR B 504 ARG 0.002 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 276 time to evaluate : 1.466 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: 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 262 LYS cc_start: 0.8038 (mmtm) cc_final: 0.7816 (mmtm) REVERT: A 310 MET cc_start: 0.7746 (tmm) cc_final: 0.7429 (tmm) REVERT: A 482 MET cc_start: 0.3321 (mtm) cc_final: 0.2212 (mtm) REVERT: A 509 GLU cc_start: 0.7362 (tt0) cc_final: 0.6713 (tt0) REVERT: A 528 ASN cc_start: 0.8037 (p0) cc_final: 0.7734 (p0) REVERT: A 551 MET cc_start: 0.7818 (mmm) cc_final: 0.7443 (mmm) REVERT: A 603 ARG cc_start: 0.7421 (mtt-85) cc_final: 0.7112 (mtt-85) REVERT: A 641 LYS cc_start: 0.8478 (tptp) cc_final: 0.8156 (tptm) REVERT: B 158 LYS cc_start: 0.7544 (mmmm) cc_final: 0.7178 (tttm) REVERT: B 187 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7865 (tm-30) REVERT: B 197 ASP cc_start: 0.7905 (m-30) cc_final: 0.7617 (m-30) REVERT: B 436 GLU cc_start: 0.7522 (pm20) cc_final: 0.7284 (mp0) REVERT: B 445 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7419 (mp0) REVERT: B 548 ASN cc_start: 0.7923 (p0) cc_final: 0.7539 (p0) REVERT: B 559 MET cc_start: 0.6718 (ppp) cc_final: 0.5778 (ppp) REVERT: B 652 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6851 (mm-30) REVERT: B 654 GLU cc_start: 0.7646 (mp0) cc_final: 0.7221 (mp0) REVERT: B 656 ASP cc_start: 0.7368 (m-30) cc_final: 0.7106 (m-30) REVERT: B 658 GLU cc_start: 0.7471 (pt0) cc_final: 0.7169 (pt0) outliers start: 9 outliers final: 8 residues processed: 278 average time/residue: 0.6023 time to fit residues: 222.3498 Evaluate side-chains 277 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 269 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 700 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10488 Z= 0.293 Angle : 0.564 5.688 14218 Z= 0.303 Chirality : 0.041 0.174 1530 Planarity : 0.004 0.039 1796 Dihedral : 4.873 19.213 1364 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.72 % Favored : 92.20 % Rotamer: Outliers : 0.99 % Allowed : 8.77 % Favored : 90.24 % 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: -1.67 (0.23), residues: 1218 helix: -0.27 (0.25), residues: 432 sheet: -2.38 (0.36), residues: 174 loop : -1.26 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 316 HIS 0.010 0.001 HIS B 285 PHE 0.013 0.001 PHE A 460 TYR 0.014 0.002 TYR B 350 ARG 0.002 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 281 time to evaluate : 1.622 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: 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 262 LYS cc_start: 0.8114 (mmtm) cc_final: 0.7886 (mmtm) REVERT: A 496 GLU cc_start: 0.6848 (tp30) cc_final: 0.6445 (tm-30) REVERT: A 509 GLU cc_start: 0.7493 (tt0) cc_final: 0.6780 (tt0) REVERT: A 512 GLN cc_start: 0.7874 (tt0) cc_final: 0.7632 (tt0) REVERT: A 528 ASN cc_start: 0.8008 (p0) cc_final: 0.7713 (p0) REVERT: A 603 ARG cc_start: 0.7469 (mtt-85) cc_final: 0.7148 (mtt-85) REVERT: A 641 LYS cc_start: 0.8512 (tptp) cc_final: 0.8212 (tptm) REVERT: B 187 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7849 (tm-30) REVERT: B 197 ASP cc_start: 0.7914 (m-30) cc_final: 0.7614 (m-30) REVERT: B 466 GLU cc_start: 0.7733 (tt0) cc_final: 0.7423 (tm-30) REVERT: B 559 MET cc_start: 0.6714 (ppp) cc_final: 0.5796 (ppp) REVERT: B 578 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7937 (mtpp) REVERT: B 652 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6818 (mm-30) REVERT: B 654 GLU cc_start: 0.7641 (mp0) cc_final: 0.7178 (mp0) REVERT: B 656 ASP cc_start: 0.7401 (m-30) cc_final: 0.7121 (m-30) REVERT: B 658 GLU cc_start: 0.7469 (pt0) cc_final: 0.7186 (pt0) outliers start: 11 outliers final: 7 residues processed: 285 average time/residue: 0.5709 time to fit residues: 217.4167 Evaluate side-chains 279 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 272 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10488 Z= 0.264 Angle : 0.558 6.113 14218 Z= 0.296 Chirality : 0.040 0.171 1530 Planarity : 0.004 0.041 1796 Dihedral : 4.808 19.388 1364 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.98 % Favored : 92.94 % Rotamer: Outliers : 1.08 % Allowed : 10.22 % Favored : 88.70 % 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: -1.69 (0.23), residues: 1218 helix: -0.31 (0.24), residues: 446 sheet: -2.53 (0.36), residues: 164 loop : -1.25 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 316 HIS 0.006 0.001 HIS B 285 PHE 0.012 0.001 PHE A 513 TYR 0.014 0.001 TYR B 693 ARG 0.002 0.000 ARG B 740 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 281 time to evaluate : 1.623 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: 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 260 LYS cc_start: 0.8513 (ttpt) cc_final: 0.8032 (ttpp) REVERT: A 262 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7863 (mmtm) REVERT: A 496 GLU cc_start: 0.6923 (tp30) cc_final: 0.6520 (tm-30) REVERT: A 509 GLU cc_start: 0.7465 (tt0) cc_final: 0.6736 (tt0) REVERT: A 512 GLN cc_start: 0.7903 (tt0) cc_final: 0.7674 (tt0) REVERT: A 528 ASN cc_start: 0.8019 (p0) cc_final: 0.7703 (p0) REVERT: A 536 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7881 (mtpp) REVERT: A 603 ARG cc_start: 0.7456 (mtt-85) cc_final: 0.7138 (mtt-85) REVERT: A 641 LYS cc_start: 0.8507 (tptp) cc_final: 0.8211 (tptm) REVERT: B 187 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 195 ARG cc_start: 0.7549 (ttm-80) cc_final: 0.7095 (ttm-80) REVERT: B 197 ASP cc_start: 0.7920 (m-30) cc_final: 0.7568 (m-30) REVERT: B 223 MET cc_start: 0.7492 (tmm) cc_final: 0.7264 (tmm) REVERT: B 436 GLU cc_start: 0.7552 (mp0) cc_final: 0.7318 (mp0) REVERT: B 466 GLU cc_start: 0.7710 (tt0) cc_final: 0.7402 (tm-30) REVERT: B 536 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7865 (mtpp) REVERT: B 548 ASN cc_start: 0.7877 (p0) cc_final: 0.7457 (p0) REVERT: B 559 MET cc_start: 0.6714 (ppp) cc_final: 0.5791 (ppp) REVERT: B 652 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6824 (mm-30) REVERT: B 654 GLU cc_start: 0.7630 (mp0) cc_final: 0.7168 (mp0) REVERT: B 656 ASP cc_start: 0.7404 (m-30) cc_final: 0.7118 (m-30) REVERT: B 658 GLU cc_start: 0.7467 (pt0) cc_final: 0.7203 (pt0) outliers start: 12 outliers final: 9 residues processed: 284 average time/residue: 0.5825 time to fit residues: 224.0118 Evaluate side-chains 284 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 275 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 700 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 10488 Z= 0.401 Angle : 0.608 6.378 14218 Z= 0.328 Chirality : 0.042 0.177 1530 Planarity : 0.004 0.049 1796 Dihedral : 5.130 20.456 1364 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.03 % Favored : 90.89 % Rotamer: Outliers : 1.45 % Allowed : 11.93 % Favored : 86.62 % 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: -2.13 (0.23), residues: 1218 helix: -0.65 (0.24), residues: 460 sheet: -2.81 (0.35), residues: 164 loop : -1.54 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 495 HIS 0.006 0.001 HIS B 285 PHE 0.021 0.002 PHE A 460 TYR 0.021 0.002 TYR A 350 ARG 0.003 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 276 time to evaluate : 1.491 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: 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 207 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8225 (mp0) REVERT: A 253 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7458 (mt-10) REVERT: A 262 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7917 (mmtm) REVERT: A 496 GLU cc_start: 0.7040 (tp30) cc_final: 0.6687 (tm-30) REVERT: A 512 GLN cc_start: 0.8014 (tt0) cc_final: 0.7714 (tt0) REVERT: A 528 ASN cc_start: 0.8065 (p0) cc_final: 0.7734 (p0) REVERT: A 558 TYR cc_start: 0.7333 (m-10) cc_final: 0.6602 (m-10) REVERT: A 603 ARG cc_start: 0.7524 (mtt-85) cc_final: 0.7213 (mtt-85) REVERT: A 641 LYS cc_start: 0.8537 (tptp) cc_final: 0.8248 (tptm) REVERT: B 187 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7836 (tm-30) REVERT: B 197 ASP cc_start: 0.7915 (m-30) cc_final: 0.7663 (m-30) REVERT: B 223 MET cc_start: 0.7480 (tmm) cc_final: 0.7277 (tmm) REVERT: B 253 GLU cc_start: 0.7637 (mp0) cc_final: 0.7350 (mp0) REVERT: B 313 GLU cc_start: 0.8245 (pm20) cc_final: 0.7997 (pm20) REVERT: B 466 GLU cc_start: 0.7725 (tt0) cc_final: 0.7436 (tm-30) REVERT: B 484 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.7114 (mtm-85) REVERT: B 559 MET cc_start: 0.6707 (ppp) cc_final: 0.5834 (ppp) REVERT: B 578 LYS cc_start: 0.8246 (mtpp) cc_final: 0.7982 (mtpp) REVERT: B 652 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6847 (mm-30) REVERT: B 654 GLU cc_start: 0.7642 (mp0) cc_final: 0.7204 (mp0) REVERT: B 656 ASP cc_start: 0.7460 (m-30) cc_final: 0.7181 (m-30) REVERT: B 658 GLU cc_start: 0.7480 (pt0) cc_final: 0.7243 (pt0) outliers start: 16 outliers final: 14 residues processed: 282 average time/residue: 0.5847 time to fit residues: 224.0814 Evaluate side-chains 286 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 272 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 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 410 ASN A 433 GLN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10488 Z= 0.203 Angle : 0.541 5.981 14218 Z= 0.285 Chirality : 0.040 0.166 1530 Planarity : 0.003 0.042 1796 Dihedral : 4.750 19.541 1364 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.54 % Allowed : 13.20 % Favored : 85.26 % 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: -1.81 (0.23), residues: 1218 helix: -0.38 (0.24), residues: 460 sheet: -2.67 (0.35), residues: 174 loop : -1.31 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 276 HIS 0.005 0.001 HIS B 139 PHE 0.024 0.001 PHE B 162 TYR 0.011 0.001 TYR B 693 ARG 0.001 0.000 ARG A 455 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 281 time to evaluate : 1.405 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: 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 168 LEU cc_start: 0.8497 (mp) cc_final: 0.8261 (mt) REVERT: A 253 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7394 (mt-10) REVERT: A 262 LYS cc_start: 0.8070 (mmtm) cc_final: 0.7857 (mmtm) REVERT: A 496 GLU cc_start: 0.6963 (tp30) cc_final: 0.6651 (tm-30) REVERT: A 512 GLN cc_start: 0.7918 (tt0) cc_final: 0.7624 (tt0) REVERT: A 551 MET cc_start: 0.7879 (mmm) cc_final: 0.7599 (mmm) REVERT: A 603 ARG cc_start: 0.7431 (mtt-85) cc_final: 0.7135 (mtt-85) REVERT: A 641 LYS cc_start: 0.8495 (tptp) cc_final: 0.8229 (tptm) REVERT: A 732 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7853 (pm20) REVERT: A 734 PHE cc_start: 0.8189 (t80) cc_final: 0.7906 (t80) REVERT: B 187 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7829 (tm-30) REVERT: B 197 ASP cc_start: 0.7846 (m-30) cc_final: 0.7574 (m-30) REVERT: B 313 GLU cc_start: 0.8229 (pm20) cc_final: 0.8013 (pm20) REVERT: B 466 GLU cc_start: 0.7719 (tt0) cc_final: 0.7439 (tm-30) REVERT: B 484 ARG cc_start: 0.7373 (mtm-85) cc_final: 0.7037 (mtm-85) REVERT: B 559 MET cc_start: 0.6686 (ppp) cc_final: 0.5835 (ppp) REVERT: B 652 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6802 (mm-30) REVERT: B 653 TRP cc_start: 0.7865 (t60) cc_final: 0.7602 (t60) REVERT: B 656 ASP cc_start: 0.7375 (m-30) cc_final: 0.7095 (m-30) REVERT: B 658 GLU cc_start: 0.7469 (pt0) cc_final: 0.7221 (pt0) outliers start: 17 outliers final: 13 residues processed: 285 average time/residue: 0.5656 time to fit residues: 216.9593 Evaluate side-chains 290 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 276 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 475 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10488 Z= 0.211 Angle : 0.540 6.555 14218 Z= 0.284 Chirality : 0.039 0.164 1530 Planarity : 0.003 0.036 1796 Dihedral : 4.686 18.988 1364 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.54 % Allowed : 14.01 % Favored : 84.45 % 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: -1.70 (0.23), residues: 1218 helix: -0.17 (0.25), residues: 448 sheet: -2.60 (0.35), residues: 174 loop : -1.33 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 679 HIS 0.005 0.001 HIS B 684 PHE 0.031 0.001 PHE B 162 TYR 0.011 0.001 TYR A 504 ARG 0.002 0.000 ARG B 643 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 285 time to evaluate : 1.559 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: 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 168 LEU cc_start: 0.8495 (mp) cc_final: 0.8258 (mt) REVERT: A 253 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7428 (mt-10) REVERT: A 262 LYS cc_start: 0.8105 (mmtm) cc_final: 0.7871 (mmtm) REVERT: A 496 GLU cc_start: 0.7003 (tp30) cc_final: 0.6701 (tm-30) REVERT: A 512 GLN cc_start: 0.7909 (tt0) cc_final: 0.7612 (tt0) REVERT: A 551 MET cc_start: 0.7867 (mmm) cc_final: 0.7640 (mmm) REVERT: A 558 TYR cc_start: 0.7297 (m-10) cc_final: 0.6440 (m-10) REVERT: A 603 ARG cc_start: 0.7447 (mtt-85) cc_final: 0.7160 (mtt-85) REVERT: A 641 LYS cc_start: 0.8503 (tptp) cc_final: 0.8248 (tptm) REVERT: A 732 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: A 734 PHE cc_start: 0.8173 (t80) cc_final: 0.7887 (t80) REVERT: A 738 MET cc_start: 0.7266 (tmm) cc_final: 0.6415 (tmm) REVERT: B 187 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7813 (tm-30) REVERT: B 197 ASP cc_start: 0.7850 (m-30) cc_final: 0.7558 (m-30) REVERT: B 466 GLU cc_start: 0.7705 (tt0) cc_final: 0.7424 (tm-30) REVERT: B 484 ARG cc_start: 0.7366 (mtm-85) cc_final: 0.7040 (mtm-85) REVERT: B 559 MET cc_start: 0.6667 (ppp) cc_final: 0.5819 (ppp) REVERT: B 578 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7845 (mtpp) REVERT: B 652 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6959 (mm-30) REVERT: B 653 TRP cc_start: 0.7928 (t60) cc_final: 0.7607 (t60) REVERT: B 656 ASP cc_start: 0.7407 (m-30) cc_final: 0.7129 (m-30) REVERT: B 658 GLU cc_start: 0.7469 (pt0) cc_final: 0.7223 (pt0) outliers start: 17 outliers final: 13 residues processed: 290 average time/residue: 0.5847 time to fit residues: 228.1243 Evaluate side-chains 295 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 281 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 688 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.0270 chunk 70 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 58 optimal weight: 0.0980 chunk 10 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10488 Z= 0.181 Angle : 0.538 6.801 14218 Z= 0.282 Chirality : 0.039 0.159 1530 Planarity : 0.003 0.040 1796 Dihedral : 4.563 18.656 1364 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.63 % Allowed : 14.74 % Favored : 83.63 % 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: -1.51 (0.24), residues: 1218 helix: 0.02 (0.25), residues: 434 sheet: -2.54 (0.35), residues: 174 loop : -1.21 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 679 HIS 0.004 0.001 HIS B 285 PHE 0.020 0.001 PHE B 162 TYR 0.011 0.001 TYR B 693 ARG 0.002 0.000 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 285 time to evaluate : 1.580 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: 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 168 LEU cc_start: 0.8480 (mp) cc_final: 0.8241 (mt) REVERT: A 253 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7415 (mt-10) REVERT: A 482 MET cc_start: 0.3585 (mtm) cc_final: 0.2297 (mtm) REVERT: A 496 GLU cc_start: 0.7019 (tp30) cc_final: 0.6716 (tm-30) REVERT: A 509 GLU cc_start: 0.7339 (tt0) cc_final: 0.6563 (tt0) REVERT: A 512 GLN cc_start: 0.7883 (tt0) cc_final: 0.7610 (tt0) REVERT: A 558 TYR cc_start: 0.7311 (m-10) cc_final: 0.6425 (m-10) REVERT: A 577 ARG cc_start: 0.7749 (tpp80) cc_final: 0.7541 (tpp80) REVERT: A 603 ARG cc_start: 0.7425 (mtt-85) cc_final: 0.7139 (mtt-85) REVERT: A 641 LYS cc_start: 0.8499 (tptp) cc_final: 0.8241 (tptm) REVERT: A 732 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7733 (pm20) REVERT: B 187 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7800 (tm-30) REVERT: B 195 ARG cc_start: 0.7494 (ttm-80) cc_final: 0.7275 (ttm-80) REVERT: B 197 ASP cc_start: 0.7838 (m-30) cc_final: 0.7568 (m-30) REVERT: B 466 GLU cc_start: 0.7674 (tt0) cc_final: 0.7412 (tm-30) REVERT: B 516 TYR cc_start: 0.8199 (t80) cc_final: 0.7975 (t80) REVERT: B 536 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7859 (mtpt) REVERT: B 559 MET cc_start: 0.6690 (ppp) cc_final: 0.5833 (ppp) REVERT: B 652 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6925 (mm-30) REVERT: B 653 TRP cc_start: 0.7905 (t60) cc_final: 0.7604 (t60) REVERT: B 656 ASP cc_start: 0.7400 (m-30) cc_final: 0.7107 (m-30) REVERT: B 658 GLU cc_start: 0.7479 (pt0) cc_final: 0.7236 (pt0) REVERT: B 704 ILE cc_start: 0.8126 (mp) cc_final: 0.7871 (mm) outliers start: 18 outliers final: 16 residues processed: 290 average time/residue: 0.5810 time to fit residues: 230.1807 Evaluate side-chains 298 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 281 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 700 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 65 optimal weight: 0.0970 chunk 47 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10488 Z= 0.185 Angle : 0.539 7.670 14218 Z= 0.282 Chirality : 0.039 0.157 1530 Planarity : 0.003 0.036 1796 Dihedral : 4.512 18.567 1364 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.63 % Allowed : 15.28 % Favored : 83.09 % 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: -1.41 (0.24), residues: 1218 helix: 0.10 (0.25), residues: 434 sheet: -2.42 (0.35), residues: 174 loop : -1.17 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 276 HIS 0.004 0.001 HIS B 684 PHE 0.017 0.001 PHE B 162 TYR 0.012 0.001 TYR B 693 ARG 0.002 0.000 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 284 time to evaluate : 1.511 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: 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 253 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7383 (mt-10) REVERT: A 512 GLN cc_start: 0.7890 (tt0) cc_final: 0.7590 (tt0) REVERT: A 558 TYR cc_start: 0.7282 (m-10) cc_final: 0.6373 (m-10) REVERT: A 577 ARG cc_start: 0.7753 (tpp80) cc_final: 0.7533 (tpp80) REVERT: A 603 ARG cc_start: 0.7422 (mtt-85) cc_final: 0.7134 (mtt-85) REVERT: A 641 LYS cc_start: 0.8539 (tptp) cc_final: 0.8288 (tptm) REVERT: A 732 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7718 (pm20) REVERT: B 187 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7800 (tm-30) REVERT: B 195 ARG cc_start: 0.7484 (ttm-80) cc_final: 0.7263 (ttm-80) REVERT: B 197 ASP cc_start: 0.7830 (m-30) cc_final: 0.7560 (m-30) REVERT: B 310 MET cc_start: 0.7958 (pmm) cc_final: 0.7584 (pmm) REVERT: B 466 GLU cc_start: 0.7661 (tt0) cc_final: 0.7451 (tm-30) REVERT: B 536 LYS cc_start: 0.8107 (mtpp) cc_final: 0.7859 (mtpt) REVERT: B 559 MET cc_start: 0.6698 (ppp) cc_final: 0.5834 (ppp) REVERT: B 652 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6929 (mm-30) REVERT: B 653 TRP cc_start: 0.7888 (t60) cc_final: 0.7589 (t60) REVERT: B 656 ASP cc_start: 0.7377 (m-30) cc_final: 0.7109 (m-30) REVERT: B 658 GLU cc_start: 0.7422 (pt0) cc_final: 0.7218 (pt0) outliers start: 18 outliers final: 17 residues processed: 290 average time/residue: 0.5607 time to fit residues: 220.4384 Evaluate side-chains 296 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 278 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 700 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 80 optimal weight: 0.3980 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10488 Z= 0.177 Angle : 0.544 7.998 14218 Z= 0.284 Chirality : 0.039 0.155 1530 Planarity : 0.003 0.039 1796 Dihedral : 4.428 18.455 1364 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.54 % Allowed : 15.37 % Favored : 83.09 % 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: -1.28 (0.24), residues: 1218 helix: 0.23 (0.26), residues: 432 sheet: -2.31 (0.35), residues: 174 loop : -1.12 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 679 HIS 0.004 0.001 HIS B 139 PHE 0.015 0.001 PHE B 162 TYR 0.012 0.001 TYR B 693 ARG 0.002 0.000 ARG B 740 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 287 time to evaluate : 1.534 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: 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 253 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7382 (mt-10) REVERT: A 496 GLU cc_start: 0.6892 (tm-30) cc_final: 0.6538 (tm-30) REVERT: A 512 GLN cc_start: 0.7862 (tt0) cc_final: 0.7586 (tt0) REVERT: A 558 TYR cc_start: 0.7285 (m-10) cc_final: 0.6451 (m-10) REVERT: A 577 ARG cc_start: 0.7751 (tpp80) cc_final: 0.7533 (tpp80) REVERT: A 603 ARG cc_start: 0.7368 (mtt-85) cc_final: 0.7088 (mtt-85) REVERT: A 641 LYS cc_start: 0.8541 (tptp) cc_final: 0.8298 (tptm) REVERT: B 152 ASP cc_start: 0.7402 (m-30) cc_final: 0.6867 (m-30) REVERT: B 187 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7785 (tm-30) REVERT: B 195 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.7261 (ttm-80) REVERT: B 197 ASP cc_start: 0.7821 (m-30) cc_final: 0.7545 (m-30) REVERT: B 310 MET cc_start: 0.7958 (pmm) cc_final: 0.7640 (pmm) REVERT: B 516 TYR cc_start: 0.8173 (t80) cc_final: 0.7967 (t80) REVERT: B 559 MET cc_start: 0.6702 (ppp) cc_final: 0.5842 (ppp) REVERT: B 652 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6918 (mm-30) REVERT: B 653 TRP cc_start: 0.7859 (t60) cc_final: 0.7570 (t60) REVERT: B 656 ASP cc_start: 0.7369 (m-30) cc_final: 0.7102 (m-30) REVERT: B 658 GLU cc_start: 0.7439 (pt0) cc_final: 0.7170 (pt0) REVERT: B 704 ILE cc_start: 0.8106 (mp) cc_final: 0.7865 (mm) outliers start: 17 outliers final: 16 residues processed: 293 average time/residue: 0.5567 time to fit residues: 220.4854 Evaluate side-chains 293 residues out of total 1106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 277 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ASP Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 667 CYS Chi-restraints excluded: chain A residue 700 ASN Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 451 PHE Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 671 ASP Chi-restraints excluded: chain B residue 674 PHE Chi-restraints excluded: chain B residue 700 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 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 = 0.4434 r_free = 0.4434 target = 0.189277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.156975 restraints weight = 45454.928| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 3.85 r_work: 0.3891 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10488 Z= 0.221 Angle : 0.554 7.964 14218 Z= 0.292 Chirality : 0.040 0.169 1530 Planarity : 0.004 0.034 1796 Dihedral : 4.523 19.084 1364 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.36 % Allowed : 15.91 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.24), residues: 1218 helix: 0.17 (0.26), residues: 432 sheet: -2.35 (0.35), residues: 174 loop : -1.14 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 679 HIS 0.004 0.001 HIS A 705 PHE 0.019 0.001 PHE A 566 TYR 0.013 0.001 TYR B 693 ARG 0.004 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5692.17 seconds wall clock time: 100 minutes 21.65 seconds (6021.65 seconds total)