Starting phenix.real_space_refine on Sat Mar 16 12:08:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ulg_42358/03_2024/8ulg_42358_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ulg_42358/03_2024/8ulg_42358.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ulg_42358/03_2024/8ulg_42358_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ulg_42358/03_2024/8ulg_42358_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ulg_42358/03_2024/8ulg_42358_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ulg_42358/03_2024/8ulg_42358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ulg_42358/03_2024/8ulg_42358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ulg_42358/03_2024/8ulg_42358_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ulg_42358/03_2024/8ulg_42358_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.063 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 Mg 2 5.21 5 S 101 5.16 5 C 9343 2.51 5 N 2462 2.21 5 O 2723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 41": "OE1" <-> "OE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 639": "OE1" <-> "OE2" Residue "B GLU 813": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14635 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6774 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 31, 'TRANS': 795} Chain: "B" Number of atoms: 6697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 824, 6697 Classifications: {'peptide': 824} Link IDs: {'PTRANS': 32, 'TRANS': 791} Chain: "C" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 540 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain breaks: 1 Chain: "D" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 542 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain breaks: 1 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, ' ZN': 1, 'IBM': 1, 'PCG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, ' ZN': 1, 'IBM': 1, 'PCG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.50, per 1000 atoms: 0.51 Number of scatterers: 14635 At special positions: 0 Unit cell: (108.54, 123.28, 168.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 101 16.00 P 2 15.00 Mg 2 11.99 O 2723 8.00 N 2462 7.00 C 9343 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.05 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" NE2 HIS A 599 " pdb="ZN ZN A 903 " - pdb=" NE2 HIS A 563 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" NE2 HIS B 597 " pdb="ZN ZN B 903 " - pdb=" NE2 HIS B 561 " 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 6 sheets defined 51.9% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 17 through 27 Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 54 through 62 Processing helix chain 'A' and resid 74 through 89 removed outlier: 3.728A pdb=" N PHE A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 205 through 250 removed outlier: 4.264A pdb=" N ASN A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N PHE A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 221 " --> pdb=" O PHE A 217 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.696A pdb=" N THR A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 414 through 458 removed outlier: 3.819A pdb=" N VAL A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASN A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) Proline residue: A 434 - end of helix removed outlier: 3.563A pdb=" N ASP A 452 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 467 Processing helix chain 'A' and resid 471 through 474 No H-bonds generated for 'chain 'A' and resid 471 through 474' Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 515 through 529 removed outlier: 3.578A pdb=" N LEU A 529 " --> pdb=" O MET A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 535 No H-bonds generated for 'chain 'A' and resid 532 through 535' Processing helix chain 'A' and resid 539 through 552 Processing helix chain 'A' and resid 561 through 576 Processing helix chain 'A' and resid 586 through 598 Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 626 through 640 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 652 through 669 removed outlier: 3.715A pdb=" N THR A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 690 removed outlier: 3.560A pdb=" N ARG A 678 " --> pdb=" O TYR A 674 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N THR A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 681 " --> pdb=" O LYS A 677 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 689 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 703 removed outlier: 4.069A pdb=" N LEU A 703 " --> pdb=" O GLN A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 720 Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 728 through 752 removed outlier: 3.732A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 779 Processing helix chain 'A' and resid 781 through 791 Processing helix chain 'A' and resid 793 through 825 removed outlier: 3.562A pdb=" N THR A 796 " --> pdb=" O GLU A 793 " (cutoff:3.500A) Proline residue: A 797 - end of helix removed outlier: 3.624A pdb=" N GLU A 825 " --> pdb=" O GLY A 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 16 through 22 removed outlier: 3.529A pdb=" N ASP B 20 " --> pdb=" O PRO B 16 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'B' and resid 47 through 68 removed outlier: 3.620A pdb=" N GLU B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 163 through 168 removed outlier: 3.792A pdb=" N LEU B 167 " --> pdb=" O PHE B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 248 removed outlier: 3.669A pdb=" N LEU B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N PHE B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLY B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 218 " --> pdb=" O ASN B 214 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 248 " --> pdb=" O ASN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 286 through 293 Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 412 through 456 removed outlier: 3.940A pdb=" N VAL B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU B 430 " --> pdb=" O GLY B 426 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASN B 431 " --> pdb=" O TRP B 427 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B 455 " --> pdb=" O MET B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 removed outlier: 3.752A pdb=" N GLN B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 465' Processing helix chain 'B' and resid 477 through 479 No H-bonds generated for 'chain 'B' and resid 477 through 479' Processing helix chain 'B' and resid 482 through 492 removed outlier: 3.743A pdb=" N GLU B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 492 " --> pdb=" O ILE B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 527 Processing helix chain 'B' and resid 529 through 532 No H-bonds generated for 'chain 'B' and resid 529 through 532' Processing helix chain 'B' and resid 537 through 550 Processing helix chain 'B' and resid 559 through 574 Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 584 through 595 Processing helix chain 'B' and resid 606 through 611 Processing helix chain 'B' and resid 615 through 619 Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.603A pdb=" N LEU B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 642 No H-bonds generated for 'chain 'B' and resid 640 through 642' Processing helix chain 'B' and resid 650 through 667 removed outlier: 3.509A pdb=" N ILE B 665 " --> pdb=" O ASP B 661 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 Processing helix chain 'B' and resid 677 through 689 removed outlier: 3.756A pdb=" N ASN B 688 " --> pdb=" O ASP B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 701 removed outlier: 4.580A pdb=" N LEU B 701 " --> pdb=" O GLU B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 718 Processing helix chain 'B' and resid 720 through 722 No H-bonds generated for 'chain 'B' and resid 720 through 722' Processing helix chain 'B' and resid 732 through 749 Processing helix chain 'B' and resid 767 through 777 Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 791 through 822 removed outlier: 3.635A pdb=" N LEU B 794 " --> pdb=" O GLU B 791 " (cutoff:3.500A) Proline residue: B 795 - end of helix Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'D' and resid 75 through 83 Processing sheet with id= A, first strand: chain 'A' and resid 105 through 110 removed outlier: 3.683A pdb=" N ARG A 93 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 95 " --> pdb=" O MET A 193 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A 189 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 182 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE A 191 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER A 180 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N MET A 193 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 178 " --> pdb=" O MET A 193 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 328 through 333 removed outlier: 3.593A pdb=" N VAL A 318 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 279 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A 318 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL A 277 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASP A 320 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N TYR A 275 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 274 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 398 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A 390 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL A 400 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET A 388 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR A 402 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 386 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR A 404 " --> pdb=" O ASN A 384 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN A 384 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 94 through 96 removed outlier: 7.160A pdb=" N LEU A 96 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N PHE A 113 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 91 through 96 removed outlier: 3.686A pdb=" N ARG B 91 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 180 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL B 189 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR B 178 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET B 191 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 176 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE B 175 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 97 through 100 Processing sheet with id= F, first strand: chain 'B' and resid 326 through 330 removed outlier: 6.848A pdb=" N LEU B 277 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL B 316 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 275 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASP B 318 " --> pdb=" O TYR B 273 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR B 273 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG B 272 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL B 396 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 388 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL B 398 " --> pdb=" O MET B 386 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET B 386 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 400 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 384 " --> pdb=" O THR B 400 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 383 " --> pdb=" O ILE B 357 " (cutoff:3.500A) 631 hydrogen bonds defined for protein. 1710 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: 4.13 Time building geometry restraints manager: 5.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2496 1.31 - 1.44: 3908 1.44 - 1.56: 8383 1.56 - 1.69: 5 1.69 - 1.81: 175 Bond restraints: 14967 Sorted by residual: bond pdb=" C6 IBM A 904 " pdb=" N1 IBM A 904 " ideal model delta sigma weight residual 1.405 1.321 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C6 IBM B 904 " pdb=" N1 IBM B 904 " ideal model delta sigma weight residual 1.405 1.322 0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C5 IBM B 904 " pdb=" C6 IBM B 904 " ideal model delta sigma weight residual 1.429 1.377 0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" C5 IBM A 904 " pdb=" C6 IBM A 904 " ideal model delta sigma weight residual 1.429 1.377 0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" C8 IBM B 904 " pdb=" N7 IBM B 904 " ideal model delta sigma weight residual 1.296 1.336 -0.040 2.00e-02 2.50e+03 4.01e+00 ... (remaining 14962 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.73: 326 105.73 - 112.80: 7798 112.80 - 119.86: 5021 119.86 - 126.92: 6897 126.92 - 133.99: 197 Bond angle restraints: 20239 Sorted by residual: angle pdb=" CB LYS A 821 " pdb=" CG LYS A 821 " pdb=" CD LYS A 821 " ideal model delta sigma weight residual 111.30 119.66 -8.36 2.30e+00 1.89e-01 1.32e+01 angle pdb=" N VAL D 66 " pdb=" CA VAL D 66 " pdb=" C VAL D 66 " ideal model delta sigma weight residual 112.29 109.23 3.06 9.40e-01 1.13e+00 1.06e+01 angle pdb=" CA LEU B 196 " pdb=" CB LEU B 196 " pdb=" CG LEU B 196 " ideal model delta sigma weight residual 116.30 127.26 -10.96 3.50e+00 8.16e-02 9.81e+00 angle pdb=" CA GLU A 444 " pdb=" CB GLU A 444 " pdb=" CG GLU A 444 " ideal model delta sigma weight residual 114.10 120.36 -6.26 2.00e+00 2.50e-01 9.79e+00 angle pdb=" N GLY C 26 " pdb=" CA GLY C 26 " pdb=" C GLY C 26 " ideal model delta sigma weight residual 112.34 118.44 -6.10 2.04e+00 2.40e-01 8.95e+00 ... (remaining 20234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 7588 17.65 - 35.29: 1064 35.29 - 52.94: 274 52.94 - 70.58: 59 70.58 - 88.23: 34 Dihedral angle restraints: 9019 sinusoidal: 3773 harmonic: 5246 Sorted by residual: dihedral pdb=" CA TYR B 402 " pdb=" C TYR B 402 " pdb=" N ASN B 403 " pdb=" CA ASN B 403 " ideal model delta harmonic sigma weight residual 180.00 156.58 23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA TYR A 404 " pdb=" C TYR A 404 " pdb=" N ASN A 405 " pdb=" CA ASN A 405 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PHE A 62 " pdb=" C PHE A 62 " pdb=" N ASP A 63 " pdb=" CA ASP A 63 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 9016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1404 0.030 - 0.059: 522 0.059 - 0.089: 164 0.089 - 0.118: 92 0.118 - 0.148: 12 Chirality restraints: 2194 Sorted by residual: chirality pdb=" CA HIS C 75 " pdb=" N HIS C 75 " pdb=" C HIS C 75 " pdb=" CB HIS C 75 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ILE C 54 " pdb=" N ILE C 54 " pdb=" C ILE C 54 " pdb=" CB ILE C 54 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE A 556 " pdb=" N ILE A 556 " pdb=" C ILE A 556 " pdb=" CB ILE A 556 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 2191 not shown) Planarity restraints: 2609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 444 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.52e+00 pdb=" CD GLU A 444 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU A 444 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 444 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 614 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 615 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 615 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 615 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 796 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A 797 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 797 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 797 " 0.025 5.00e-02 4.00e+02 ... (remaining 2606 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 127 2.64 - 3.21: 13331 3.21 - 3.77: 22192 3.77 - 4.34: 29778 4.34 - 4.90: 50526 Nonbonded interactions: 115954 Sorted by model distance: nonbonded pdb=" OD2 ASP B 598 " pdb="ZN ZN B 903 " model vdw 2.079 2.230 nonbonded pdb=" O ILE A 556 " pdb=" ND2 ASN A 560 " model vdw 2.232 2.520 nonbonded pdb=" O PHE A 289 " pdb=" NZ LYS B 675 " model vdw 2.235 2.520 nonbonded pdb=" OD2 ASP A 92 " pdb=" OH TYR A 172 " model vdw 2.235 2.440 nonbonded pdb=" O CYS A 163 " pdb=" O1A PCG A 901 " model vdw 2.256 2.440 ... (remaining 115949 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 'C' and (resid 11 through 39 or resid 49 through 87)) selection = (chain 'D' and resid 11 through 87) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.170 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 40.770 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 14967 Z= 0.188 Angle : 0.560 10.964 20239 Z= 0.285 Chirality : 0.039 0.148 2194 Planarity : 0.004 0.051 2609 Dihedral : 18.166 88.230 5619 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 0.06 % Allowed : 20.33 % Favored : 79.61 % 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: 1.30 (0.20), residues: 1777 helix: 2.00 (0.17), residues: 951 sheet: 0.37 (0.46), residues: 138 loop : -0.67 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 559 HIS 0.005 0.000 HIS A 599 PHE 0.022 0.001 PHE B 11 TYR 0.010 0.001 TYR B 223 ARG 0.009 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 MET cc_start: 0.8775 (mmm) cc_final: 0.8334 (mmm) REVERT: C 15 ARG cc_start: 0.9249 (tpp80) cc_final: 0.8693 (mmm-85) REVERT: C 83 GLN cc_start: 0.9131 (tm-30) cc_final: 0.8708 (tm-30) REVERT: D 12 SER cc_start: 0.9058 (t) cc_final: 0.8855 (p) REVERT: D 15 ARG cc_start: 0.8766 (mtt90) cc_final: 0.8491 (mtm110) REVERT: D 16 VAL cc_start: 0.9214 (t) cc_final: 0.8285 (t) REVERT: D 74 ASN cc_start: 0.8931 (t0) cc_final: 0.8397 (t0) REVERT: D 76 LEU cc_start: 0.9742 (tp) cc_final: 0.9513 (mt) REVERT: D 78 LEU cc_start: 0.9738 (tp) cc_final: 0.9177 (mt) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.3061 time to fit residues: 61.8307 Evaluate side-chains 115 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 137 optimal weight: 0.0670 chunk 53 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14967 Z= 0.161 Angle : 0.505 8.718 20239 Z= 0.263 Chirality : 0.039 0.158 2194 Planarity : 0.004 0.047 2609 Dihedral : 4.663 92.263 1953 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 1.63 % Allowed : 20.26 % Favored : 78.11 % 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: 1.39 (0.21), residues: 1777 helix: 2.00 (0.17), residues: 958 sheet: 0.59 (0.45), residues: 142 loop : -0.56 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 480 HIS 0.004 0.000 HIS A 599 PHE 0.012 0.001 PHE C 38 TYR 0.012 0.001 TYR B 319 ARG 0.005 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.7744 (m-10) cc_final: 0.7523 (m-10) REVERT: A 71 ASN cc_start: 0.8249 (p0) cc_final: 0.7939 (p0) REVERT: A 183 MET cc_start: 0.8940 (mmm) cc_final: 0.8165 (tmm) REVERT: A 193 MET cc_start: 0.8342 (mtp) cc_final: 0.8069 (ttm) REVERT: A 440 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8284 (mmm) REVERT: A 760 MET cc_start: 0.8890 (tmm) cc_final: 0.8594 (tmm) REVERT: B 438 MET cc_start: 0.8700 (mmt) cc_final: 0.8475 (mmt) REVERT: C 15 ARG cc_start: 0.9215 (tpp80) cc_final: 0.8746 (mtt90) REVERT: C 77 GLU cc_start: 0.9301 (pt0) cc_final: 0.8904 (pt0) REVERT: C 83 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8568 (tm-30) REVERT: D 12 SER cc_start: 0.9059 (t) cc_final: 0.8826 (p) REVERT: D 16 VAL cc_start: 0.8835 (t) cc_final: 0.8469 (t) REVERT: D 36 ARG cc_start: 0.8661 (mpp-170) cc_final: 0.8345 (mpp-170) REVERT: D 39 LYS cc_start: 0.8009 (mmmt) cc_final: 0.7684 (mmpt) REVERT: D 74 ASN cc_start: 0.8997 (t0) cc_final: 0.8435 (t0) outliers start: 26 outliers final: 10 residues processed: 140 average time/residue: 0.2790 time to fit residues: 58.1128 Evaluate side-chains 125 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 64 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 128 optimal weight: 0.0670 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14967 Z= 0.146 Angle : 0.484 7.758 20239 Z= 0.249 Chirality : 0.038 0.157 2194 Planarity : 0.004 0.047 2609 Dihedral : 4.585 91.840 1953 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 1.56 % Allowed : 20.83 % Favored : 77.61 % 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 (0.21), residues: 1777 helix: 1.98 (0.18), residues: 959 sheet: 0.68 (0.44), residues: 142 loop : -0.51 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 480 HIS 0.005 0.000 HIS D 75 PHE 0.011 0.001 PHE C 38 TYR 0.011 0.001 TYR B 97 ARG 0.003 0.000 ARG B 531 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.7792 (m-10) cc_final: 0.7586 (m-10) REVERT: A 71 ASN cc_start: 0.8379 (p0) cc_final: 0.8031 (p0) REVERT: A 136 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9087 (tt) REVERT: A 183 MET cc_start: 0.8924 (mmm) cc_final: 0.8318 (mmm) REVERT: A 193 MET cc_start: 0.8343 (mtp) cc_final: 0.8136 (ttm) REVERT: A 440 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8265 (mmm) REVERT: A 760 MET cc_start: 0.8957 (tmm) cc_final: 0.8552 (tmm) REVERT: A 761 MET cc_start: 0.8599 (mmt) cc_final: 0.8380 (mmt) REVERT: C 15 ARG cc_start: 0.9192 (tpp80) cc_final: 0.8712 (mmm-85) REVERT: C 17 MET cc_start: 0.8009 (mmt) cc_final: 0.7751 (mmp) REVERT: C 77 GLU cc_start: 0.9232 (pt0) cc_final: 0.8880 (pt0) REVERT: C 83 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8576 (tm-30) REVERT: D 15 ARG cc_start: 0.8783 (mtt90) cc_final: 0.8577 (mtp180) REVERT: D 16 VAL cc_start: 0.8855 (t) cc_final: 0.8473 (t) REVERT: D 36 ARG cc_start: 0.8594 (mpp-170) cc_final: 0.8307 (mpp-170) outliers start: 25 outliers final: 10 residues processed: 140 average time/residue: 0.3131 time to fit residues: 64.6418 Evaluate side-chains 127 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 64 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 3.9990 chunk 120 optimal weight: 0.0470 chunk 83 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 170 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 141 optimal weight: 4.9990 overall best weight: 1.3660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 828 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14967 Z= 0.188 Angle : 0.493 7.502 20239 Z= 0.252 Chirality : 0.038 0.154 2194 Planarity : 0.004 0.047 2609 Dihedral : 4.624 94.305 1953 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 2.06 % Allowed : 20.33 % Favored : 77.61 % 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: 1.43 (0.21), residues: 1777 helix: 2.01 (0.18), residues: 964 sheet: 0.65 (0.44), residues: 145 loop : -0.55 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 480 HIS 0.003 0.000 HIS C 75 PHE 0.016 0.001 PHE A 62 TYR 0.011 0.001 TYR B 97 ARG 0.004 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.7848 (m-10) cc_final: 0.7624 (m-10) REVERT: A 71 ASN cc_start: 0.8500 (p0) cc_final: 0.8056 (p0) REVERT: A 136 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9101 (tt) REVERT: A 183 MET cc_start: 0.8945 (mmm) cc_final: 0.8562 (mmm) REVERT: A 193 MET cc_start: 0.8342 (mtp) cc_final: 0.8059 (ttm) REVERT: A 760 MET cc_start: 0.8966 (tmm) cc_final: 0.8525 (tmm) REVERT: C 15 ARG cc_start: 0.9151 (tpp80) cc_final: 0.8786 (mmm-85) REVERT: C 17 MET cc_start: 0.8065 (mmt) cc_final: 0.7800 (mmp) REVERT: C 83 GLN cc_start: 0.9116 (tm-30) cc_final: 0.8682 (tm-30) REVERT: D 15 ARG cc_start: 0.8750 (mtt90) cc_final: 0.8527 (mtp180) REVERT: D 16 VAL cc_start: 0.9108 (t) cc_final: 0.8820 (t) REVERT: D 36 ARG cc_start: 0.8615 (mpp-170) cc_final: 0.8318 (mpp-170) REVERT: D 39 LYS cc_start: 0.8014 (mmmt) cc_final: 0.7652 (mmpt) REVERT: D 76 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9469 (mm) outliers start: 33 outliers final: 23 residues processed: 140 average time/residue: 0.2809 time to fit residues: 58.5290 Evaluate side-chains 140 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 76 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 145 optimal weight: 0.3980 chunk 117 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14967 Z= 0.141 Angle : 0.479 8.692 20239 Z= 0.243 Chirality : 0.038 0.169 2194 Planarity : 0.004 0.046 2609 Dihedral : 4.532 91.380 1953 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.63 % Allowed : 21.33 % Favored : 77.05 % 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: 1.44 (0.21), residues: 1777 helix: 1.99 (0.18), residues: 964 sheet: 0.71 (0.44), residues: 145 loop : -0.51 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.003 0.000 HIS A 599 PHE 0.012 0.001 PHE A 62 TYR 0.010 0.001 TYR B 97 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.7811 (m-10) cc_final: 0.7583 (m-10) REVERT: A 71 ASN cc_start: 0.8454 (p0) cc_final: 0.7985 (p0) REVERT: A 82 MET cc_start: 0.9137 (mmm) cc_final: 0.8929 (mmm) REVERT: A 136 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9006 (tt) REVERT: A 183 MET cc_start: 0.8990 (mmm) cc_final: 0.8549 (mmm) REVERT: A 193 MET cc_start: 0.8304 (mtp) cc_final: 0.8043 (ttm) REVERT: A 760 MET cc_start: 0.8950 (tmm) cc_final: 0.8729 (tmm) REVERT: C 15 ARG cc_start: 0.9149 (tpp80) cc_final: 0.8803 (mtt90) REVERT: C 83 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8698 (tm-30) REVERT: D 15 ARG cc_start: 0.8736 (mtt90) cc_final: 0.8501 (mtp180) REVERT: D 36 ARG cc_start: 0.8566 (mpp-170) cc_final: 0.8117 (mpp-170) REVERT: D 73 PHE cc_start: 0.7389 (m-80) cc_final: 0.7041 (m-80) REVERT: D 76 LEU cc_start: 0.9731 (OUTLIER) cc_final: 0.9449 (mm) outliers start: 26 outliers final: 16 residues processed: 133 average time/residue: 0.2834 time to fit residues: 55.6201 Evaluate side-chains 125 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 76 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 0.0470 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 0.0370 chunk 14 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 overall best weight: 0.9758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14967 Z= 0.157 Angle : 0.490 9.229 20239 Z= 0.247 Chirality : 0.038 0.174 2194 Planarity : 0.004 0.046 2609 Dihedral : 4.527 93.270 1953 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.06 % Allowed : 20.76 % Favored : 77.17 % 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: 1.48 (0.21), residues: 1777 helix: 2.01 (0.18), residues: 963 sheet: 0.75 (0.44), residues: 145 loop : -0.47 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.003 0.000 HIS A 599 PHE 0.011 0.001 PHE A 62 TYR 0.010 0.001 TYR B 97 ARG 0.004 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8550 (p0) cc_final: 0.8066 (p0) REVERT: A 136 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8993 (tt) REVERT: A 183 MET cc_start: 0.8956 (mmm) cc_final: 0.8590 (mmm) REVERT: C 15 ARG cc_start: 0.9182 (tpp80) cc_final: 0.8820 (mtt90) REVERT: C 83 GLN cc_start: 0.9131 (tm-30) cc_final: 0.8727 (tm-30) REVERT: D 15 ARG cc_start: 0.8731 (mtt90) cc_final: 0.8519 (mtp180) REVERT: D 36 ARG cc_start: 0.8589 (mpp-170) cc_final: 0.8255 (mpp-170) REVERT: D 76 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9461 (mm) outliers start: 33 outliers final: 25 residues processed: 137 average time/residue: 0.2697 time to fit residues: 56.0935 Evaluate side-chains 135 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 76 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14967 Z= 0.168 Angle : 0.502 10.421 20239 Z= 0.253 Chirality : 0.038 0.199 2194 Planarity : 0.004 0.048 2609 Dihedral : 4.533 92.794 1953 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.19 % Allowed : 20.89 % Favored : 76.92 % 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: 1.52 (0.21), residues: 1777 helix: 2.03 (0.18), residues: 965 sheet: 0.80 (0.44), residues: 145 loop : -0.45 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.003 0.000 HIS A 599 PHE 0.013 0.001 PHE D 73 TYR 0.010 0.001 TYR B 97 ARG 0.003 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 113 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8511 (p0) cc_final: 0.8021 (p0) REVERT: A 82 MET cc_start: 0.9273 (mmm) cc_final: 0.9063 (mmm) REVERT: A 136 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8992 (tt) REVERT: A 183 MET cc_start: 0.8970 (mmm) cc_final: 0.8694 (mmm) REVERT: A 592 MET cc_start: 0.8993 (mmm) cc_final: 0.8424 (mmt) REVERT: A 712 MET cc_start: 0.8872 (ttt) cc_final: 0.8326 (tpt) REVERT: A 760 MET cc_start: 0.8937 (tmm) cc_final: 0.8549 (tmm) REVERT: C 15 ARG cc_start: 0.9181 (tpp80) cc_final: 0.8823 (mtt90) REVERT: C 83 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8754 (tm-30) REVERT: D 15 ARG cc_start: 0.8656 (mtt90) cc_final: 0.8451 (mtp180) REVERT: D 36 ARG cc_start: 0.8594 (mpp-170) cc_final: 0.8128 (mpp-170) REVERT: D 39 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7720 (mmpt) REVERT: D 76 LEU cc_start: 0.9739 (OUTLIER) cc_final: 0.9478 (mm) outliers start: 35 outliers final: 25 residues processed: 140 average time/residue: 0.2823 time to fit residues: 58.4776 Evaluate side-chains 137 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 76 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 115 optimal weight: 0.0770 chunk 83 optimal weight: 0.0570 chunk 15 optimal weight: 0.0980 chunk 133 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14967 Z= 0.138 Angle : 0.513 13.101 20239 Z= 0.255 Chirality : 0.038 0.195 2194 Planarity : 0.004 0.046 2609 Dihedral : 4.489 92.511 1953 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.56 % Allowed : 21.64 % Favored : 76.80 % 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: 1.52 (0.21), residues: 1777 helix: 2.00 (0.18), residues: 965 sheet: 0.91 (0.44), residues: 145 loop : -0.43 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.003 0.000 HIS A 599 PHE 0.016 0.001 PHE D 73 TYR 0.011 0.001 TYR B 97 ARG 0.005 0.000 ARG B 692 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8507 (p0) cc_final: 0.7984 (p0) REVERT: A 82 MET cc_start: 0.9202 (mmm) cc_final: 0.9001 (mmm) REVERT: A 136 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8961 (tt) REVERT: A 183 MET cc_start: 0.8986 (mmm) cc_final: 0.8769 (mmm) REVERT: A 760 MET cc_start: 0.8975 (tmm) cc_final: 0.8583 (tmm) REVERT: C 15 ARG cc_start: 0.9168 (tpp80) cc_final: 0.8818 (mmm-85) REVERT: C 83 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8738 (tm-30) REVERT: D 17 MET cc_start: 0.8657 (mmt) cc_final: 0.8414 (mmm) REVERT: D 76 LEU cc_start: 0.9740 (OUTLIER) cc_final: 0.9494 (mm) outliers start: 25 outliers final: 20 residues processed: 128 average time/residue: 0.2882 time to fit residues: 54.7730 Evaluate side-chains 124 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 76 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14967 Z= 0.158 Angle : 0.517 9.219 20239 Z= 0.259 Chirality : 0.038 0.181 2194 Planarity : 0.004 0.056 2609 Dihedral : 4.522 92.669 1953 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.69 % Allowed : 21.83 % Favored : 76.49 % 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: 1.54 (0.21), residues: 1777 helix: 2.02 (0.18), residues: 966 sheet: 0.88 (0.44), residues: 145 loop : -0.42 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 70 HIS 0.003 0.000 HIS A 599 PHE 0.019 0.001 PHE D 73 TYR 0.011 0.001 TYR B 97 ARG 0.011 0.000 ARG A 652 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8504 (p0) cc_final: 0.7951 (p0) REVERT: A 136 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9011 (tt) REVERT: A 183 MET cc_start: 0.9009 (mmm) cc_final: 0.8796 (mmm) REVERT: A 760 MET cc_start: 0.8969 (tmm) cc_final: 0.8555 (tmm) REVERT: C 15 ARG cc_start: 0.9173 (tpp80) cc_final: 0.8815 (mtt90) REVERT: C 83 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8767 (tm-30) REVERT: D 17 MET cc_start: 0.8672 (mmt) cc_final: 0.8430 (mmm) REVERT: D 76 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9497 (mm) outliers start: 27 outliers final: 21 residues processed: 123 average time/residue: 0.2804 time to fit residues: 50.8733 Evaluate side-chains 126 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 76 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 175 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14967 Z= 0.152 Angle : 0.514 10.704 20239 Z= 0.256 Chirality : 0.038 0.163 2194 Planarity : 0.004 0.046 2609 Dihedral : 4.503 91.846 1953 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.44 % Allowed : 21.95 % Favored : 76.61 % 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: 1.55 (0.21), residues: 1777 helix: 2.00 (0.18), residues: 967 sheet: 0.89 (0.44), residues: 145 loop : -0.37 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.003 0.000 HIS A 599 PHE 0.014 0.001 PHE D 73 TYR 0.010 0.001 TYR B 97 ARG 0.009 0.000 ARG A 652 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3554 Ramachandran restraints generated. 1777 Oldfield, 0 Emsley, 1777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASN cc_start: 0.8500 (p0) cc_final: 0.7941 (p0) REVERT: A 136 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9009 (tt) REVERT: A 760 MET cc_start: 0.8880 (tmm) cc_final: 0.8503 (tmm) REVERT: B 72 MET cc_start: 0.8271 (tmm) cc_final: 0.7968 (tmm) REVERT: C 15 ARG cc_start: 0.9163 (tpp80) cc_final: 0.8811 (mtt90) REVERT: C 83 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8752 (tm-30) REVERT: D 76 LEU cc_start: 0.9779 (OUTLIER) cc_final: 0.9529 (mm) outliers start: 23 outliers final: 18 residues processed: 128 average time/residue: 0.2800 time to fit residues: 53.1625 Evaluate side-chains 124 residues out of total 1599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 435 ASP Chi-restraints excluded: chain A residue 480 TRP Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 694 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 76 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 0.0370 chunk 58 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.0670 chunk 122 optimal weight: 0.0980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.042369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.030611 restraints weight = 84578.469| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 4.59 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14967 Z= 0.143 Angle : 0.518 9.414 20239 Z= 0.257 Chirality : 0.038 0.161 2194 Planarity : 0.004 0.048 2609 Dihedral : 4.481 91.475 1953 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.25 % Allowed : 22.33 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.21), residues: 1777 helix: 1.98 (0.18), residues: 967 sheet: 0.88 (0.44), residues: 144 loop : -0.35 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.003 0.000 HIS A 599 PHE 0.014 0.001 PHE D 73 TYR 0.008 0.001 TYR B 97 ARG 0.007 0.000 ARG A 652 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2612.18 seconds wall clock time: 48 minutes 19.08 seconds (2899.08 seconds total)